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  • 1.
    Begum, Shamima
    et al.
    University of Manchester, England.
    Cianci, Michele
    DESY, Germany.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Falklöf, Olle
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Haedener, Alfons
    University of Manchester, England.
    Helliwell, John R.
    University of Manchester, England.
    Helliwell, Madeleine
    University of Manchester, England.
    Regan, Andrew C.
    University of Manchester, England.
    Watt, Ian F.
    University of Manchester, England.
    On the origin and variation of colors in lobster carapace2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 26, s. 16723-16732Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The chemical basis of the blue-black to pink-orange color change on cooking of lobster, due to thermal denaturation of an astaxanthin-protein complex, alpha-crustacyanin, in the lobster carapace, has so far been elusive. Here, we investigate the relaxation of the astaxanthin pigment from its bound enolate form to its neutral hydroxyketone form, as origin of the spectral shift, by analyzing the response of UV-vis spectra of a water-soluble 3-hydroxy-4-oxo-beta-ionone model of astaxanthin to increases in pH, and by performing extensive quantum chemical calculations over a wide range of chemical conditions. The enolization of astaxanthin is consistent with the X-ray diffraction data of beta-crustacyanin (PDB code: 1GKA) whose crystals possess the distinct blue color. We find that enolate formation is possible within the protein environment and associated with a large bathochromic shift, thus offering a cogent explanation for the blue-black color and the response to thermal denaturation and revealing the chemistry of astaxanthin upon complex formation.

  • 2.
    Borg, O. Anders
    et al.
    Uppsala University, Sweden.
    Durbeej, Bo
    University of Siena, Italy.
    Relative ground and excited-state pKa values of phytochromobilin in the photoactivation of phytochrome: a computational study2007Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, nr 39, s. 11554-11565Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The conversion of the plant photoreceptor phytochrome from an inactive (Pr) to an active form (Pfr) is accomplished by a red-light induced Z  E photoisomerization of its phytochromobilin chromophore. In recent years, the question whether the photoactivation involves a change in chromophore protonation state has been the subject of many experimental studies. Here, we have used quantum chemical methods to calculate relative ground and excited-state pKa values of the different pyrrole moieties of phytochromobilin in a protein-like environment. Assuming (based on experimental data) a Pr ZaZsZa chromophore and considering isomerizations at C15 and C5, it is found that moieties B and C are the strongest acids both in the ground state and in the bright first singlet excited state, which is rationalized in simple geometric and electronic terms. It is also shown that neither light absorption nor isomerization increases the acidity of phytochromobilin relative to the reference Pr state with all pyrrolenic nitrogens protonated. Hence, provided that the subset of chromophore geometries under investigation is biologically relevant, there appears to be no intrinsic driving force for a proton-transfer event. In a series of benchmark calculations, the performance of ab initio and time-dependent density functional theory methods for excited-state studies of phytochromobilin is evaluated in light of available experimental data.

  • 3.
    Borg, O. Anders
    et al.
    Uppsala University, Sweden.
    Durbeej, Bo
    University of Siena, Italy.
    Which factors determine the acidity of the phytochromobilin chromophore of plant phytochrome?2008Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, nr 18, s. 2528-2537Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Quantum chemical calculations aimed at identifying the factors controlling the acidity of phytochromobilin, the tetrapyrrole chromophore of the plant photoreceptor phytochrome, are reported. Phytochrome is converted from an inactive (Pr) to an active form (Pfr) through a series of events initiated by a Z  E photoisomerization of phytochromobilin, forming the Lumi-R intermediate, and much controversy exists as to whether the protonation state of the chromophore (cationic in Pr with all nitrogens protonated) changes during the photoactivation. Here, relative ground (S0) and excited-state (S1) pKas of all four pyrrole moieties of phytochromobilin in all 64 possible configurations with respect to the three methine bridges are calculated in a protein-like environment, using a recently benchmarked level of theory. Accordingly, the relationships between acidity and chromophore geometry and charge distribution, hydrogen bonding, and light absorption are investigated in some detail, and discussed in terms of possible mechanisms making a proton transfer reaction more probable along the Pr  Pfr reaction than in the parent cationic Pr state. It is found that charge distribution in the cationic species, intra-molecular hydrogen bonding in the neutral, and hydrogen bonding with two highly conserved aspartate and histidine residues have a significant effect on the acidity, while overall chromophore geometry and electronic state are less important factors. Furthermore, based on the calculations, two processes that may facilitate a proton transfer by substantially lowering the pKas relative to their Pr values are identified: (i) a thermal Z,anti  Z,syn isomerization at C5, occurring after formation of Lumi-R; (ii) a perturbation of the hydrogen bonding network which in Pr comprises the nitrogens of pyrroles A, B and C and the two aspartate and histidine residues.

  • 4.
    Borg, O. Anders
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Örebro University, Sweden.
    Durbeej, Bo
    University of Siena, Italy.
    Electron-transfer induced repair of 6-4 photoproducts in DNA: a computational study2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 12, s. 2351-2361Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C–N and C–C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

  • 5.
    Bucher, Denis
    et al.
    University of Sydney.
    M Sandala, Gregory
    University of Sydney.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Radom, Leo
    University of Sydney.
    Smith, David M
    Rudjer Boskovic Institute.
    The elusive 5'-deoxyadenosyl radical in coenzyme-B12-mediated reactions2012Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, nr 3, s. 1591-1599Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Vitamin B12 and its biologically active counterparts possess the only examples of carbon-cobalt bonds in living systems. The role of such motifs as radical reservoirs has potential application in future catalytic and electronic nanodevices. To fully understand radical generation in coenzyme B12 (dAdoCbl)-dependent enzymes, however, major obstacles still need to be overcome. In this work, we have used Car-Parrinello molecular dynamics (CPMD) simulations, in a mixed quantum mechanics/molecular mechanics (QM/MM) framework, to investigate the initial stages of the methylmalonyl-CoA-mutase-catalyzed reaction. We demonstrate that the 5'-deoxyadenosyl radical (dAdo(center dot)) exists as a distinct entity in this reaction, consistent with the results of extensive experimental and some previous theoretical studies. We report free energy calculations and first-principles trajectories enzymes catalyze coenzyme activation and control highly reactive radical intermediates. that help understand how B12 enzymes catalyze coenzyme activation and control highly reactive radical intermediates.

  • 6.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    A computational perspective on the photochemistry of photosensory proteins: phytochromes and Anabaena sensory rhodopsin2012Ingår i: Quantum Simulations of Materials and Biological Systems / [ed] Jun Zeng, Rui-Qin Zhang and Herbert R. Treutlein, Springer Netherlands, 2012, s. 169-194Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    The merits of quantum simulations in photobiology are illustrated by presenting recent computational studies investigating the basic photochemistry of phytochromes, a ubiquitous family of photosensory proteins, and Anabaena sensory rhodopsin, a recently discovered member of the rhodopsins. Focusing on the chromophore photoisomerization reactions that trigger these proteins’ responses to light and using density functional methods and multiconfigurational ab initio methods in combination with molecular mechanics, three surprising results can be singled out. First, it is found that the photochemical reactivity of the bilin chromophores of phytochromes is fundamentally different in solution and in the protein, with different photoisomerization channels being preferred. Second, it is found that the two retinal photoisomerizations that govern the interconversion of Anabaena sensory rhodopsin between its two major forms proceed in such a way that the chromophore completes a full 360° rotation during one photocycle. This means that this protein is a biological realization of a light-driven molecular rotor. Third, and finally, it is demonstrated that the stereochemical origin of this remarkable behavior is actually a key element for the function of a class of synthetic light-driven molecular rotors developed from overcrowded alkenes, thereby identifying Anabaena sensory rhodopsin as a possible source of inspiration for the future design and construction of such molecular machines.

  • 7.
    Durbeej, Bo
    University of Siena, Italy and Uppsala University, Sweden.
    On the primary event of phytochrome: quantum chemical comparison of photoreactions at C4, C10 and C152009Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, nr 9, s. 1354-1361Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phytochromes are widespread photoreceptors responsive to red and far-red light that exist in two photochromic forms Pr (inactive) and Pfr (active). The Pr  Pfr conversion proceeds through a series of events initiated by Z  E photoisomerization of the tetrapyrrole chromophore, believed to occur at C15 of the methine bridge between rings C and D. Recent crystal structures show that ring D in Pr is less tightly packed by the protein than rings A, B and C, which should favor the C15 reaction over reactions at C4 (AB methine bridge) and C10 (BC). In the present work, quantum chemical methods are used to establish the intrinsic reactivity of the chromophore towards all three possible Z  E isomerization events in the absence of steric effects and specific interactions with the protein. Using a level of theory that reproduces spectroscopic data with anaccuracy of 0.2 eV, it is demonstrated that isolated conditions allow the C10 photoreaction to substantially dominate. This finding suggests that the different degrees of ring-packing observed inthe protein are crucial not only to facilitate a reaction at C15, but also to prevent an intrinsically more favorable reaction at C10 from taking place.

  • 8.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden and University of Sydney, Australia.
    Borg, O. Anders
    Uppsala University, Sweden.
    Eriksson, Leif A
    Örebro University, Sweden.
    Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome2005Ingår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 416, nr 1-3, s. 83-88Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The photoactivation of the plant photoreceptor phytochrome is governed by a red-light-induced C15-Z  C15-E isomerization of the tetrapyrrolic chromophore phytochromobilin. From the viewpoint of experimental studies, ambiguity prevails as to whether the photoactivation involves a proton transfer from the chromophore to the surrounding protein. Here, we report a theoretical study addressing the effect of phytochromobilin protonation state on its photoisomerization by means of quantum chemical calculations. It is found that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form − a finding which supports the view that phytochromobilin remains protonated during phytochrome photoactivation.

  • 9.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Borg, O. Anders
    Uppsala University, Sweden .
    Eriksson, Leif A
    Uppsala University, Sweden and Örebro University, Sweden.
    Phytochromobilin C15-Z,syn → C15-E,anti isomerization: concerted or stepwise?2004Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, nr 21, s. 5066-5073Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The C15-Z,syn  C15-E,anti isomerization of phytochromobilin that underlies the photoactivation of phytochrome, the plant photoreceptor responsive to red and far-red light, is investigated by means of quantum chemical methods. By calculating ground and excited-state potential energy surfaces for a phytochromobilin model comprising the full tetrapyrrolic skeleton, and taking into consideration rotations around the C14–C15 and C15=C16 bonds constituting the methine bridge between pyrrole rings C and D, it is found that a stepwise Z  E, syn  anti mechanism is energetically preferable over a concerted Z,syn  E,anti mechanism. In particular, on the basis of the calculated potential energy surfaces, it is proposed that the primary photochemical reaction involves a Z  E isomerization only, and that the subsequent syn  anti isomerization proceeds thermally.

  • 10.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    A density functional theory study of coniferyl alcohol intermonomeric cross linkages in lignin – three-dimensional structures, stabilities and the thermodynamic control hypothesis2003Ingår i: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 57, nr 2, s. 150-164Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Density functional theory methods are utilized to investigate structural features and stabilities of the most common lignin dimerization products. It is found that intra-molecular hydrogen bonding acts as a stabilizing force in the lowest-energy conformer(s) of several different dimeric lignin structures. Furthermore, the calculations show that the hypothesis of thermodynamic control of monolignol dimerization accounts for some of the results obtained in experimental studies aimed at determining the ratios of intermonomeric linkages. A quantitative correlation between experimentally observed ratios and calculated relative energies cannot, however, be pointed out.

  • 11.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A
    Uppsala University, Sweden and Örebro University, Sweden .
    Conformational dependence of the electronic absorption by astaxanthin and its implications for the bathochromic shift in crustacyanin2004Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, nr 16, s. 4190-4198Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The conformational dependence of the electronic absorption by astaxanthin is believed to be of relevance for the bathochromic shift that this carotenoid assumes upon binding to crustacyanin, the protein macromolecular complex responsible for the slate-blue colouration of lobster shell. Here, we report quantum chemical calculations suggesting that the bathochromic shift that can be attributed to changes in astaxanthin conformation brought about by binding to the protein in fact is rather small. In particular, by subjecting an exhaustive set of different astaxanthin conformations to time-dependent density functional theory (TD-DFT) and semiempirical configuration interaction singles (ZINDO/S) calculations, it is found that the bathochromic shift due to the protein-enforced coplanarity of the β-ionone rings with the polyene chain is considerably smaller (TD-DFT: 22–37 nm; ZINDO/S: 11–19 nm) than the >100 nm shift that recently [B. Durbeej and L. A. Eriksson, Chem. Phys. Lett., 2003, 375, 30] was predicted to arise from a hydrogen-bond mediated interaction involving one of the astaxanthin C4 keto groups and a histidine residue of the surrounding protein. Moreover, the calculations suggest that the protein-induced bowing of astaxanthin about the center of the polyene chain is of no relevance for the observed bathochromic shift.

  • 12.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Formation of β-O-4 lignin models – a theoretical study2003Ingår i: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 57, nr 5, s. 466-478Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The formation of two different β-O-4 lignin models is investigated by means of density functional calculations. It is found that the coupling of two coniferyl alcohol radicals forming a quinone methide proceeds by an energy barrier of ~2–5 kcal/mol, and that the associated reaction energy is negative by more than 20 kcal/mol. On the basis of the corresponding results obtained for the coupling of a coniferyl alcohol radical to a coniferyl alcohol, it is argued that the resulting radical, albeit being formed in an energetically less favourable process, might play an important role in lignin polymerisation. Finally, two different reaction mechanisms for the conversion of a quinone methide into a guaiacylglycerol-β-coniferyl ether dilignol through the addition of water are explored.

  • 13.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study2003Ingår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 375, nr 1-2, s. 30-38Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The structural origin of the bathochromic shift assumed by the electronic absorption spectrum of protein-bound astaxanthin, the carotenoid that upon binding to crustacyanin is responsible for the blue colouration of lobster shell, is investigated by means of quantum chemical methods. The calculations suggest that the bathochromic shift is largely due to one of the astaxanthin C4 keto groups being hydrogen-bonded to a histidine residue of the surrounding protein, and that the effect of this histidine is directly dependent on its protonation state. Out of the different methodologies (CIS, TD-DFT, and ZINDO/S) employed to calculate wavelengths of maximum absorption, the best agreement with experimental data is obtained using the semiempirical ZINDO/S method.

  • 14.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    On the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: why are thymines more reactive?2003Ingår i: Photochemistry and Photobiology, ISSN 0031-8655, E-ISSN 1751-1097, Vol. 78, nr 2, s. 159-167Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The reaction pathways for thermal and photochemical formation of cyclobutane pyrimidine dimers in DNA are explored using density functional theory techniques. Although it is found that the thermal [2+2] cycloadditions of thymine + thymine (T + T  T<>T), cytosine +  cytosine (C + C  C<>C) and cytosine + thymine (C + T  C<>T) all are similarly unfavorable in terms of energy barriers and reaction energies, the excited-state energy curves associated with the corresponding photochemical cycloadditions display differences that – in line with experimental findings – unanimously point to the predominance of T<>T in UV-irradiated DNA. It is shown that the photocycloaddition of thymines is facilitated by the fact that the S1 state of the corresponding reactant complex lies comparatively high in energy. Moreover, at a nuclear configuration coinciding with the ground-state transition structure, the excited-state energy curve displays an absolute minimum only for the T + T system. Finally, the T + T system is also associated with the most favorable excited-state energy barriers and has the smallest S2–S0 energy gap at the ground-state transition structure.

  • 15.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Örebro University, Sweden.
    Photodegradation of substituted stilbene compounds: what colors aging paper yellow?2005Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, nr 25, s. 5677-5682Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Photodegradation of lignin is one of the major postprocessing problems in paper production, as this renders yellowing of the paper and reduced paper quality. In this study, we have explored the photochemical properties of substituted stilbene derivatives believed to be key chromophores in the photodegradation of lignin derived from cinnamyl alcohol. In particular, the present work focuses on the computation of UV/vis electronic absorption spectra for different methoxylated stilbenes and their proposed photodegradation products. All calculations were performed using the time-dependent formalism of density functional theory (TD-DFT) and the B3LYP hybrid functional. It is concluded that the methodology employed is capable of reproducing not only the overall spectra, but also subtle features owing to the effects of different substitution patterns. For the strongly absorbing first excited singlet state (HOMO  LUMO excitation) of the methoxylated stilbenes, the calculated transition energies are, albeit somewhat fortuitously, in excellent agreement with experimental data. The light-induced yellowing indirectly caused by the presence of stilbenes can be rationalized in terms of the absorption spectra of the resulting photodegraded o-quinones, for which distinct transitions in the 420–500 nm region of the visible spectrum lacking prior to degradation are observed.

  • 16.
    Durbeej, Bo
    et al.
    University of Siena, Italy.
    Eriksson, Leif A.
    Örebro University, Sweden.
    Protein-bound chromophores astaxanthin and phytochromobilin: excited state quantum chemical studies2006Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 8, nr 35, s. 4053-4071Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present an overview of excited state quantum chemical calculations aimed at elucidating controversial issues regarding the photochemistry of the protein-bound chromophores astaxanthin and phytochromobilin. In particular, we show how the application of time-dependent density functional theory and other single-reference quantum chemical excited state methods have contributed to shed new light on the origin of the >0.5 eV bathochromic shift of the electronic absorption by the carotenoid astaxanthin in the protein macromolecular complex crustacyanin, and the mechanism for C15-Z,syn  C15-E,anti isomerization of the tetrapyrrole phytochromobilin that underlies the photoactivation of the plant photoreceptor phytochrome. Within the approximation that exciton coupling is neglected, the calculations on astaxanthin provide support for the notion that the bathochromic shift, which is responsible for the slate-blue coloration of lobster shell, is due to polarization rather than a conformational change of the chromophore in the protein-bound state. Furthermore, the polarization is attributed to a hydrogen-bonded protonated histidine residue. The calculations on phytochromobilin, in turn, suggest that a stepwise C15-Z,syn  C15-E,syn (photochemical), C15-E,syn  C15-E,anti (thermal) mechanism is much more favorable than a concerted, fully photochemical mechanism, and that neutral forms of the chromophore are much less likely to photoisomerize than the parent, protonated form. Accordingly, the calculations indirectly support the view that the photoactivation of phytochrome does not involve a proton transfer from the chromophore to the surrounding protein.

  • 17.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Reaction mechanism of thymine dimer formation in DNA induced by UV light2002Ingår i: Journal of Photochemistry and Photobiology A: Chemistry, ISSN 1010-6030, E-ISSN 1873-2666, Vol. 152, nr 1-3, s. 95-101Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The formation of thymine dimers in DNA is investigated by means of density functional theory (DFT) techniques. While it is found that a thermally induced [2 + 2] cycloaddition reaction proceeds via a very high energy transition state (80–88 kcal/mol above the reactant complex), the energy barrier for UV light induced formation – explored within the time-dependent DFT formalism – is only a few kilocalories per mol. As such, these results serve as an illustrative example of how UV radiation may induce DNA lesions. For the reactant complex, the calculated vertical excitation energy corresponding to the S1  S0 transition (  *) lies in the far-UV region, in accordance with experimental data.

  • 18.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals2003Ingår i: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 57, nr 1, s. 59-61Artikel i tidskrift (Refereegranskat)
  • 19.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Thermodynamics of the photoenzymic repair mechanism studied by density functional theory2000Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 122, nr 41, s. 10126-10132Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The thermodynamics of the different steps in the photoenzymic fragmentation of a thymine dimer is investigated using density functional theory (DFT) methods, including time-dependent (TD) DFT for calculating electronic transition energies, employing a model system consisting of different thymine derivatives and enzymatic cofactors (FADH, 8-HDF, and MTHF). It is found that the crucial electron-transfer steps, as well as the overall reaction, are exothermic and that the splitting of the C6−C6’ bond in a thymine dimer radical anion is slightly exothermic (2.4 kcal mol−1 ) with a 2.3 kcal mol−1 energy barrier. The reaction energies assigned to the different steps are generally in good agreement with the corresponding energies from previous estimates that have constituted the foundation of the proposed reaction mechanism. On the basis of this comparison, the results support the proposed model. Moreover, the excellent agreement between theoretical excitation energies and experimental data shows that TDDFT can be successfully applied to large organic molecules.

  • 20.
    Durbeej, Bo
    et al.
    University of Sydney, Australia and Uppsala University, Sweden.
    Sandala, Gregory M
    University of Sydney, Australia.
    Bucher, Denis
    University of Sydney, Australia.
    Smith, David M.
    Rudjer Boskovic Institute, Zagreb, Croatia.
    Radom, Leo
    University of Sydney, Australia.
    On the importance of ribose orientation in the substrate activation of coenzyme B12-dependent mutases2009Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, nr 34, s. 8578-8585Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The degree to which the corrin ring portion of coenzyme B12 can facilitate the H-atom-abstraction step in the glutamate mutase (GM)-catalyzed reaction of (S)-glutamate has been investigated with density functional theory. The crystal structure of GM identifies two possible orientations of the ribose portion of coenzyme B12. In one orientation (A), the OH groups of the ribose extend away from the corrin ring, whereas in the other orientation (B) the OH groups, especially that involving O3’, are instead directed towards the corrin ring. Our calculations identify a sizable stabilization amounting to about 30 kJ mol–1 in the transition structure (TS) complex corresponding to orientation B (TSBCorIm). In the TS complex where the ribose instead is positioned in orientation A, no such effect is manifested. The observed stabilization in TSBCorIm appears to be the result of favorable interactions involving O3’ and the corrin ring, including a C–H···O hydrogen bond. We find that the degree of stabilization is not particularly sensitive to the Co–C distance. Our calculations show that any potential stabilization afforded to the H-atom abstraction step by coenzyme B12 is sensitive to the orientation of the ribose moiety.

  • 21.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Wang, Yan-Ni
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Lignin biosynthesis and degradation − a major challenge for computational chemistry2003Ingår i: High Performance Computing for Computational Science — VECPAR 2002, Springer Berlin/Heidelberg, 2003, Vol. 2565, s. 137-165Konferensbidrag (Refereegranskat)
    Abstract [en]

    In the present chapter we review a series of computational studies related to lignin biosynthesis and degradation, with the aim to understand at a molecular level processes crucial to paper and pulp industries. Due to the complexity of the problem, a wide variety of computational approaches are employed, each with its own merits. From the theoretical studies we are able to draw conclusions regarding the behavior of lignol monomers and their corresponding dehydrogenated radicals in aqueous solution and in lipid bilayers, and reaction mechanisms, conformations and relative stabilities of lignol dimers.

  • 22.
    Falklöf, Olle
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Deciphering Excited-State Protonation and Tautomeric States of Oxyluciferin through Calculation of Excited-State Equilibrium Constants2013Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    This study investigates the excited-state equilibria of the chemiexcited oxyluciferin light emitter responsible for the emission of light in firefly bioluminescence. To date, there is no consensus regarding which of the possible chemical forms connected by excited-state keto-enol and acid-base equilibrium reactions that is the main contributor to the light emission. Using a hybrid cluster-continuum approach, we perform quantum chemical calculations to obtain the relevant excited-state pKE and pKa values in aqueous solution. As such, we gain insight into the intrinsic tendency of the chemiexcited oxyluciferin light emitter to prefer a particular form.

  • 23.
    Falklöf, Olle
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants2014Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, nr 30, s. 2184-2194Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Although recent years have seen much progress in the elucidation of the mechanisms underlying the bioluminescence of fireflies, there is to date no consensus on the precise contributions to the light emission from the different possible forms of the chemiexcited oxyluciferin (OxyLH(2)) cofactor. Here, this problem is investigated by the calculation of excited-state equilibrium constants in aqueous solution for keto-enol and acid-base reactions connecting six neutral, monoanionic and dianionic forms of OxyLH(2). Particularly, rather than relying on the standard Forster equation and the associated assumption that entropic effects are negligible, these equilibrium constants are for the first time calculated in terms of excited-state free energies of a Born-Haber cycle. Performing quantum chemical calculations with density functional theory methods and using a hybrid cluster-continuum approach to describe solvent effects, a suitable protocol for the modeling is first defined from benchmark calculations on phenol. Applying this protocol to the various OxyLH(2) species and verifying that available experimental data (absorption shifts and ground-state equilibrium constants) are accurately reproduced, it is then found that the phenolate-keto-OxyLH(-) monoanion is intrinsically the preferred form of OxyLH(2) in the excited state, which suggests a potential key role for this species in the bioluminescence of fireflies.

  • 24.
    Falklöf, Olle
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Modeling of phytochrome absorption spectra2013Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, nr 16, s. 1363-1374Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

  • 25.
    Falklöf, Olle
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome2015Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Phytochromes constitute a superfamily of photoreceptor proteins that exist in two forms that absorb red (Pr) and far-red (Pfr) light. The conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the bilin chromophore at the C15-C16 bond of the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on a highresolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions prevent photoisomerization at any other site than the C15-C16 bond. The tendency of phytochromes to always isomerize at this very bond would thus be explained by steric effects.

  • 26.
    Falklöf, Olle
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study2013Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, s. 19-28Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

  • 27.
    Falklöf, Olle
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Steric Effects Govern the Photoactivation of Phytochromes2016Ingår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 17, nr 7, s. 954-957Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phytochromes constitute a superfamily of photoreceptor proteins existing in two forms that absorb red (Pr) and far-red (Pfr) light. Although it is well-known that the conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the linear tetrapyrrole chromophore, direct evidence is scarce as to why this reaction always occurs at the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics calculations based on a high-resolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions render photoisomerizations at the AB and BC bridges much less probable than photoisomerization at the CD bridge.

  • 28.
    Falklöf, Olle
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Norman, Patrick
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin2015Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, nr 49, s. 11911-11921Artikel i tidskrift (Refereegranskat)
    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, 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 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 two to five orders of magnitude smaller than the nonradiative ones.

  • 29.
    Fang, Changfeng
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Oruganti, Baswanth
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Computational study of the working mechanism and rate acceleration of overcrowded alkene-based light-driven rotary molecular motors2014Ingår i: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 4, nr 20, s. 10240-10251Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In recent years, much progress has been made in the design, synthesis and operation of light-driven rotary molecular motors based on chiral overcrowded alkenes. Through consecutive cistrans photoisomerization and thermal helix inversion steps, where the latter dictate the overall rate of rotation, these motors achieve a full 360° unidirectional rotation around the carbon–carbon double bond connecting the two (rotator and stator) alkene halves. In this work, we report quantum chemical calculations indicating that a particularly fast-rotating overcrowded alkene-based motor capable of reaching the MHz regime, can be made to rotate even faster by the substitution of a rotator methyl group with a methoxy group. Specifically, using density functional theory methods that reproduce the rate-limiting 35 kJ mol−1 thermal free-energy barriers shown by the methyl-bearing motor with errors of 5 kJ mol−1 only, it is predicted that this substitution reduces these barriers by a significant 15–20 kJ mol−1. This prediction is preceded by a series of benchmark calculations for assessing how well density functional theory methods account for available experimental data (crystallographic, UV-vis absorption, thermodynamic) on the rotary cycles of overcrowded alkenes, and a detailed examination of the thermal and photochemical reaction mechanisms of the original motor of this type.

  • 30.
    Fang, Changfeng
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Oruganti, Baswanth
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    How method-dependent are calculated differences between vertical, adiabatic, and 0-0 excitation energies?2014Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, nr 23, s. 4157-4171Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Through a large number of benchmark studies, the performance of different quantum chemical methods in calculating vertical excitation energies is today quite well established. Furthermore, these efforts have in recent years been complemented by a few benchmarks focusing instead on adiabatic excitation energies. However, it is much less well established how calculated differences between vertical, adiabatic and 0-0 excitation energies vary between methods, which may be due to the cost of evaluating zero-point vibrational energy corrections for excited states. To fill this gap, we have calculated vertical, adiabatic, and 0-0 excitation energies for a benchmark set of molecules covering both organic and inorganic systems. Considering in total 96 excited states and using both TD-DFT with a variety of exchange-correlation functionals and the ab initio CIS and CC2 methods, it is found that while the vertical excitation energies obtained with the various methods show an average (over the 96 states) standard deviation of 0.39 eV, the corresponding standard deviations for the differences between vertical, adiabatic, and 0-0 excitation energies are much smaller: 0.10 (difference between adiabatic and vertical) and 0.02 eV (difference between 0-0 and adiabatic). These results provide a quantitative measure showing that the calculation of such quantities in photochemical modeling is well amenable to low-level methods. In addition, we also report on how these energy differences vary between chemical systems and assess the performance of TD-DFT, CIS, and CC2 in reproducing experimental 0-0 excitation energies.

  • 31.
    Oruganti, Baswanth
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Fang, Changfeng
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten. Jining University, Peoples R China.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk kemi. Linköpings universitet, Tekniska fakulteten.
    Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects2015Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 33, s. 21740-21751Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report a systematic computational investigation of the possibility to accelerate the rate-limiting thermal isomerizations of the rotary cycles of synthetic light-driven overcrowded alkene-based molecular motors through modulation of steric interactions. Choosing as a reference system a second-generation motor known to accomplish rotary motion in the MHz regime and using density functional theory methods, we propose a three-step mechanism for the thermal isomerizations of this motor and show that variation of the steric bulkiness of the substituent at the stereocenter can reduce the (already small) free-energy barrier of the rate-determining step by a further 15-17 kJ mol(-1). This finding holds promise for future motors of this kind to reach beyond the MHz regime. Furthermore, we demonstrate and explain why one particular step is kinetically favored by decreasing and another step is kinetically favored by increasing the steric bulkiness of this substituent, and identify a possible back reaction capable of impeding the rotary rate.

  • 32.
    Strambi, Angela
    et al.
    University of Siena, Italy .
    Durbeej, Bo
    Uppsala University, Sweden.
    Excited-state modeling of the astaxanthin dimer predicts a minor contribution from exciton coupling to the bathochromic shift in crustacyanin2009Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, nr 15, s. 5311-5317Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The >0.50 eV bathochromic shift of the absorption by the carotenoid astaxanthin in crustacyanin, the carotenoprotein responsible for the coloration of lobster shell, is believed to result from ground-state polarization of the chromophore and/or exciton coupling between the two chromophores of each protein subunit. Here, the contribution of exciton coupling to the shift is quantified using quantum chemical calculations that do not rely on the dipole-dipole approximation but rather consider the full astaxanthin dimer in the geometry relevant for the protein-bound state. Employing a variety of methods, it is found that the exciton coupling amounts to 0.04 eV only. Furthermore, even when more closely aggregated dimers than the one in the protein are considered, the predicted couplings remain small (0.05-0.09 eV). These findings demonstrate that the bathochromic shift cannot be explained in terms of exciton coupling. It is therefore argued that polarization is likely to be the dominant mechanism, a notion supported by the fact that calculations carried out at the same levels of theory identify a scenario (hydrogen bonding with a histidine residue) whose contribution to the shift vastly exceeds that of exciton coupling.

  • 33.
    Strambi, Angela
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Initial excited-state relaxation of the bilin chromophores of phytochromes: a computational study2011Ingår i: PHOTOCHEMICAL and PHOTOBIOLOGICAL SCIENCES, ISSN 1474-905X, Vol. 10, nr 4, s. 569-579Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The geometric relaxation following light absorption of the biliverdin, phycocyanobilin and phytochromobilin tetrapyrrole chromophores of bacterial, cyanobacterial and plant phytochromes has been investigated using density functional theory methods. Considering stereoisomers relevant for both red-absorbing Pr and far-red-absorbing Pfr forms of the photoreceptor, it is found that the initial excited-state evolution is dominated by torsional motion at the C10-C11 bond. This holds true for all three chromophores and irrespective of which configuration the chromophores adopt. This finding suggests that the photochromic cycling of phytochromes between their Pr and Pfr forms, which is known to be governed by Z/E photoisomerizations at the C15-C16 bond, relies on interactions between the chromophore and the protein to prevent photoisomerizations at C10-C11. Further, it is found that the uneven distribution of positive charge between the pyrrole rings is a major factor for the photochemical reactivity of the C10-C11 bond.

  • 34.
    Strambi, Angela
    et al.
    University of Siena, Department of Chemistry.
    Durbeej, Bo
    University of Siena, Department of Chemistry.
    Ferre, Nicolas
    University of Provence.
    Olivucci, Massimo
    University of Siena, Department of Chemistry.
    Anabaena sensory rhodopsin is a light-driven unidirectional rotor2010Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, nr 50, s. 21322-21326Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The implementation of multiconfigurational quantum chemistry methods into a quantum-mechanics/molecular-mechanics protocol has allowed the construction of a realistic computer model for the sensory rhodopsin of the cyanobacterium Anabaena PCC 7120. The model, which reproduces the absorption spectra of both the all-trans and 13-cis forms of the protein and their associated K and L intermediates, is employed to investigate the light-driven steps of the photochromic cycle exhibited by the protein. It is found that the photoisomerizations of the all-trans and 13-cis retinal chromophores occur through unidirectional, counterclockwise 180 deg rotations of the =C14-C15= moiety with respect to the Lys210-linked end of the chromophore axis. Thus, the sequential interconversions of the all-trans and 13-cis forms during a single photochromic cycle yield a complete (360 deg) unidirectional rotation of the =C14-C15= moiety. This finding implies that Anabaena sensory rhodopsin is a biological realization of a light-driven molecular rotor.

  • 35.
    Uppsten, Malin
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
    Quantum chemical comparison of vertical, adiabatic, and 0-0 excitation energies: The PYP and GFP chromophores2012Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, nr 23, s. 1892-1901Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A number of benchmark studies investigating the performance of quantum chemical methods for calculating vertical excitation energies are today available in the literature. However, less established is the variation between methods in their estimates of the differences between vertical, adiabatic, and 0-0 excitation energies. To this end, such excitation energies are here calculated for the bright S1 states of the anionic chromophores of the photoactive yellow protein (PYP) and the green fluorescent protein (GFP) in the gas phase using configuration interaction singles, complete active space self-consistent field, coupled-cluster singles and doubles, and time-dependent density functional theory methods. Although the estimates of the excitation energies vary by more than 1 eV between the methods, the differences between the different types of excitation energies are found to be relatively method-insensitive, varying by ∼0.1 eV only for these particular chromophores. Specifically, the adiabatic energies are uniformly 0.10–0.17 (PYP) and 0.06–0.17 eV (GFP) lower than the vertical energies, and the 0-0 energies are similarly 0.09–0.14 (PYP) and 0.07–0.17 eV (GFP) lower than the adiabatic energies.

  • 36.
    Wang, Jun
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    Toward Fast and Efficient Visible-Light-Driven Molecular Motors: A Minimal Design2018Ingår i: ChemistryOpen, ISSN 2191-1363, Vol. 7, nr 8, s. 583-589Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A key goal in the development of light-driven rotary molecular motors is to facilitate their usage in biology and medicine by shifting the required irradiation wavelengths from the UV regime to the nondestructive visible regime. Although some progress has been made toward this goal, most available visible-light-driven motors either have relatively low quantum yields or require that thermal steps follow the photoisomerizations that underlie the rotary motion. Here, a minimal design for visible-light-driven motors without these drawbacks is presented and evaluated on the basis of state-of-the-art quantum chemical calculations and molecular dynamics simulations. The design, featuring dihydropyridinium and cyclohexenylidene motifs and comprising only five conjugated double bonds, is found to produce a full 360° rotation through fast photoisomerizations (excited-state lifetimes of ≈ 170-250 fs) powered by photons with energies well below 3 eV. 

  • 37.
    Wang, Jun
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    Oruganti, Baswanth
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    A Straightforward Route to Aromatic Excited States in Molecular Motors that Improves Photochemical Efficiency2019Ingår i: ChemPhotoChem, ISSN 2367-0932, Vol. 3, nr 6, s. 450-460Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The many successful efforts to optimize the thermal steps that are part of the reaction cycles of most light-driven rotary molecular motors have not been followed by studies providing a similarly detailed understanding of how the efficiency of the photochemical steps that actually power the motors can be improved. Against this background, we herein use computational methods to investigate the merits of an approach to increase the quantum yields of E/Z-photoisomerization-based motors by enabling one of their two moieties to become aromatic in the photoactive excited state. Through quantum chemical calculations, a straightforward route to excited states of this type is found for motors where one moiety can be transformed into an aromatic anion by an electron donor at the other moiety. Furthermore, through molecular dynamics simulations, motors operated in such excited states are indeed predicted to be much more efficient than similar motors operated in the absence of excited-state aromaticity. 

  • 38.
    Zhang, Jun
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Wang, Jun
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    Sandberg, Alexander
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Wu, Xiongyu
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Nyström, Sofie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    LeVine, Harry III
    Sanders-Brown Center on Aging, University of Kentucky, KY 40536-0230, Lexington, USA..
    Konradsson, Peter
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Hammarström, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Durbeej, Bo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    Lindgren, Mikael
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten. Department of Physics, Norwegian University of Science and Technology, 7491, Trondheim, Norway..
    Intramolecular Proton and Charge Transfer of Pyrene-based trans-Stilbene Salicylic Acids Applied to Detection of Aggregated Proteins.2018Ingår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, nr 22, s. 3001-3009Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Two analogues to the fluorescent amyloid probe 2,5-bis(4'-hydroxy-3'-carboxy-styryl)benzene (X-34) were synthesized based on the trans-stilbene pyrene scaffold (Py1SA and Py2SA). The compounds show strikingly different emission spectra when bound to preformed Aβ1-42 fibrils. This remarkable emission difference is retained when bound to amyloid fibrils of four distinct proteins, suggesting a common binding configuration for each molecule. Density functional theory calculations show that Py1SA is twisted, while Py2SA is more planar. Still, an analysis of the highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs) of the two compounds indicates that the degree of electronic coupling between the pyrene and salicylic acid (SA) moieties is larger in Py1SA than in Py2SA. Excited state intramolecular proton transfer (ESIPT) coupled-charge transfer (ICT) was observed for the anionic form in polar solvents. We conclude that ICT properties of trans-stilbene derivatives can be utilized for amyloid probe design with large changes in emission spectra and decay times from analogous chemical structures depending on the detailed physical nature of the binding site.less thanbr /greater than (© 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim.)

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