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  • 1.
    Arpa Gonzalez, Enrique Manuel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    HOMER: a reparameterization of the harmonic oscillator model of aromaticity (HOMA) for excited states2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 25, no 25, p. 16763-16771Article in journal (Refereed)
    Abstract [en]

    Excited-state aromaticity (ESA) and antiaromaticity (ESAA) are by now well-established concepts for explaining photophysical properties and photochemical reactivities of cyclic, conjugated molecules. However, their application is less straightforward than the corresponding process by which the thermal chemistry of such systems is rationalized in terms of ground-state aromaticity (GSA) and antiaromaticity (GSAA). Recognizing that the harmonic oscillator model of aromaticity (HOMA) provides an easy way to measure aromaticity on geometric grounds, it is therefore notable that this model is yet to be parameterized for excited states. Against this background, we here present a new parameterization of HOMA - termed HOMER - for the T-1 state of both carbocyclic and heterocyclic compounds based on high-level quantum-chemical calculations. Considering CC, CN, NN and CO bonds and testing the parametrization using calculated magnetic data as reference, we find that the description of ESA and ESAA by HOMER is superior to that afforded by the original HOMA scheme, and that it reaches the same overall quality as HOMA does for GSA and GSAA. Furthermore, we demonstrate that the derived HOMER parameters can be used for predictive modeling of ESA and ESAA at very different levels of theory. Altogether, the results highlight the potential of HOMER to facilitate future studies of ESA and ESAA.

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  • 2.
    Arpa Gonzalez, Enrique Manuel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    A Proof-of-Principle Design for Through-Space Transmission of Unidirectional Rotary Motion by Molecular Photogears2023In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765Article in journal (Refereed)
    Abstract [en]

    The construction of molecular photogears that can achieve through-space transmission of the unidirectional double-bond rotary motion of light-driven molecular motors onto a remote single-bond axis is a formidable challenge in the field of artificial molecular machines. Here, we present a proof-of-principle design of such photogears that is based on the possibility of using stereogenic substituents to control both the relative stabilities of two helical forms of the photogear and the double-bond photoisomerization reaction that connects them. The potential of the design was verified by quantum-chemical modeling through which photogearing was found to be a favorable process compared to free-standing single-bond rotation ("slippage"). Overall, our study unveils a surprisingly simple approach to realizing unidirectional photogearing. A stereochemical approach to transmitting the directional double-bond rotary motion of light-driven molecular motors through space onto a remote single-bond axis is put forth and successfully tested by means of quantum-chemical modeling. A key result in the assessment of the approach is that the desired photogearing process is favorable compared to the undesired, free-standing single-bond rotation process ("slippage") with which it competes.**image

  • 3.
    Arpa González, Enrique Manuel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    In Silico Design of Dihydroazulene/Vinylheptafulvene Photoswitches for Solar-Energy Storage Guided by an All-Around Performance Descriptor2023In: Chemistry−Methods, ISSN 2628-9725, Vol. 3, article id e202200060Article in journal (Refereed)
    Abstract [en]

    A major challenge in the development of molecular photoswitches capable of storing and releasing solar energy is to simultaneously realize many of the performance criteria required of the switches for such applications. Here, we take on this challenge by introducing an all-around performance descriptor that combines three key criteria (related to energy density, storage time and light-absorption characteristics), and by using density functional theory methods to calculate its values for 52 newly designed dihydroazulene/vinylheptafulvene (DHA/VHF) switches. Thereby, we are able to identify several switches with excellent overall properties that contain a structural motif absent in all DHA/VHF compounds previously considered for solar-energy storage. For some of these switches, we also provide retrosynthetic analyses and demonstrate that they form the energy-storing VHF isomer through a facile DHA!VHF photoisomerization reaction. All in all, we conclude that these switches show great promise for further development towards applications in solar-energy storage.

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  • 4.
    Arpa González, Enrique Manuel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Transient changes in aromaticity and their effect on excited-state proton transfer reactions2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 19, p. 11496-11500Article in journal (Refereed)
    Abstract [en]

    The common approach to investigate the impact of aromaticity on excited-state proton transfer by probing the (anti)aromatic character of reactants and products alone is scrutinized by modelling such reactions involving 2-pyridone. Thereby, it is found that energy barriers can be strongly influenced by transient changes in aromaticity unaccounted for by this approach, particularly when the photoexcited state interacts with a second excited state. Overall, the modelling identifies a pronounced effect overlooked by most studies on this topic.

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  • 5.
    Begum, Shamima
    et al.
    University of Manchester, England.
    Cianci, Michele
    DESY, Germany.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Falklöf, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    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 carapace2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 26, p. 16723-16732Article in journal (Refereed)
    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.

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  • 6.
    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 study2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 39, p. 11554-11565Article in journal (Refereed)
    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.

  • 7.
    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?2008In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 18, p. 2528-2537Article in journal (Refereed)
    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.

  • 8.
    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 study2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 12, p. 2351-2361Article in journal (Refereed)
    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.

  • 9.
    Bucher, Denis
    et al.
    University of Sydney.
    M Sandala, Gregory
    University of Sydney.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Radom, Leo
    University of Sydney.
    Smith, David M
    Rudjer Boskovic Institute.
    The elusive 5'-deoxyadenosyl radical in coenzyme-B12-mediated reactions2012In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, no 3, p. 1591-1599Article in journal (Refereed)
    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.

  • 10.
    Corpas, Javier
    et al.
    Univ Autonoma Madrid UAM, Spain.
    Gomez-Mendoza, Miguel
    IMDEA Energy Inst, Spain.
    Arpa Gonzalez, Enrique Manuel
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    de la Pena OShea, Victor A.
    IMDEA Energy Inst, Spain.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Carretero, Juan C.
    Univ Autonoma Madrid UAM, Spain.
    Mauleon, Pablo
    Univ Autonoma Madrid UAM, Spain.
    Arrayas, Ramon Gomez
    Univ Autonoma Madrid UAM, Spain.
    Iterative Dual-Metal and Energy Transfer Catalysis Enables Stereodivergence in Alkyne Difunctionalization: Carboboration as Case Study2023In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 13, no 22, p. 14914-14927Article in journal (Refereed)
    Abstract [en]

    Stereochemically defined tetrasubstituted olefins are widespread structural elements of organic molecules and key intermediates in organic synthesis. However, flexible methods enabling stereodivergent access to E and Z isomers of fully substituted alkenes from a common precursor represent a significant challenge and are actively sought after in catalysis, especially those amenable to complex multifunctional molecules. Herein, we demonstrate that iterative dual-metal and energy transfer catalysis constitutes a unique platform for achieving stereodivergence in the difunctionalization of internal alkynes. The utility of this approach is showcased by the stereodivergent synthesis of both stereoisomers of tetrasubstituted beta-boryl acrylates from internal alkynoates with excellent stereocontrol via sequential carboboration and photoisomerization. The reluctance of electron-deficient internal alkynes to undergo catalytic carboboration has been overcome through cooperative Cu/Pd-catalysis, whereas an Ir complex was identified as a versatile sensitizer that is able to photoisomerize the resulting sterically crowded alkenes. Mechanistic studies by means of quantum-chemical calculations, quenching experiments, and transient absorption spectroscopy have been applied to unveil the mechanism of both steps.

  • 11.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    A computational perspective on the photochemistry of photosensory proteins: phytochromes and Anabaena sensory rhodopsin2012In: Quantum Simulations of Materials and Biological Systems / [ed] Jun Zeng, Rui-Qin Zhang and Herbert R. Treutlein, Springer Netherlands, 2012, p. 169-194Chapter in book (Refereed)
    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.

  • 12.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Competing Excited-State Deactivation Processes in Bacteriophytochromes2020In: Chemical Physics and Quantum Chemistry / [ed] Kenneth Ruud, Erkki J. Brändas, Elsevier, 2020, Vol. 81, p. 243-268Chapter in book (Refereed)
    Abstract [en]

    Bacteriophytochromes are photoreceptor proteins of widespread use as templates for the engineering of fluorescent proteins with emission maxima in the near-infrared regime beyond 650 nm ideally suited for deep-tissue imaging of living cells. The main challenge for such engineering is that native bacteriophytochromes have very low fluorescence quantum yields because of competing excited-state deactivation processes, which include both the well-known photoisomerization reaction of their linear tetrapyrrole chromophore and excited-state proton transfer reactions from the chromophore to the surrounding protein. Here, we describe how hybrid quantum mechanics/molecular mechanics modeling of the photochemistry of these proteins has provided valuable guidelines for strengthening the fluorescence through inhibition of the competing non-radiative processes. Specifically, based on the results of such modeling, we present a strategy to inhibit the photoisomerization on steric grounds and identify the most probable proton transfer reaction to exert a negative influence on the fluorescence quantum yields. It is our hope that these results will help stimulate further contributions from quantum chemistry toward realizing the potential for entirely new bioimaging applications commonly attributed to brightly near-infrared fluorescent bacteriophytochromes.

  • 13.
    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 C152009In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, no 9, p. 1354-1361Article in journal (Refereed)
    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.

  • 14.
    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 phytochrome2005In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 416, no 1-3, p. 83-88Article in journal (Refereed)
    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.

  • 15.
    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?2004In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, no 21, p. 5066-5073Article in journal (Refereed)
    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.

  • 16.
    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 hypothesis2003In: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 57, no 2, p. 150-164Article in journal (Refereed)
    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.

  • 17.
    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 crustacyanin2004In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 6, no 16, p. 4190-4198Article in journal (Refereed)
    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.

  • 18.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Formation of β-O-4 lignin models – a theoretical study2003In: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 57, no 5, p. 466-478Article in journal (Refereed)
    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.

  • 19.
    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 study2003In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 375, no 1-2, p. 30-38Article in journal (Refereed)
    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.

  • 20.
    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?2003In: Photochemistry and Photobiology, ISSN 0031-8655, E-ISSN 1751-1097, Vol. 78, no 2, p. 159-167Article in journal (Refereed)
    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.

  • 21.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Örebro University, Sweden.
    Photodegradation of substituted stilbene compounds: what colors aging paper yellow?2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 25, p. 5677-5682Article in journal (Refereed)
    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.

  • 22.
    Durbeej, Bo
    et al.
    University of Siena, Italy.
    Eriksson, Leif A.
    Örebro University, Sweden.
    Protein-bound chromophores astaxanthin and phytochromobilin: excited state quantum chemical studies2006In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 8, no 35, p. 4053-4071Article in journal (Refereed)
    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.

  • 23.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Reaction mechanism of thymine dimer formation in DNA induced by UV light2002In: Journal of Photochemistry and Photobiology A: Chemistry, ISSN 1010-6030, E-ISSN 1873-2666, Vol. 152, no 1-3, p. 95-101Article in journal (Refereed)
    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.

  • 24.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals2003In: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 57, no 1, p. 59-61Article in journal (Refereed)
  • 25.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Uppsala University, Sweden.
    Thermodynamics of the photoenzymic repair mechanism studied by density functional theory2000In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 122, no 41, p. 10126-10132Article in journal (Refereed)
    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.

  • 26.
    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 mutases2009In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 34, p. 8578-8585Article in journal (Refereed)
    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.

  • 27.
    Durbeej, Bo
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Wang, Jun
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Oruganti, Baswanth
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Molecular Photoswitching Aided by Excited-State Aromaticity2018In: ChemPlusChem, E-ISSN 2192-6506, Vol. 83, no 11, p. 958-967Article in journal (Refereed)
    Abstract [en]

    Central to the development of optoelectronic devices is the availability of efficient synthetic molecular photoswitches, the design of which is an arena where the evolving concept of excited‐state aromaticity (ESA) is yet to make a big impact. The aim of this minireview is to illustrate the potential of this concept to become a key tool for the future design of photoswitches. The paper starts with a discussion of challenges facing the use of photoswitches for applications and continues with an account of how the ESA concept has progressed since its inception. Then, following some brief remarks on computational modeling of photoswitches and ESA, the paper describes two different approaches to improve the quantum yields and response times of switches driven by E/Z photoisomerization or photoinduced H‐atom/proton transfer reactions through simple ESA considerations. It is our hope that these approaches, verified by quantum chemical calculations and molecular dynamics simulations, will help stimulate the application of the ESA concept as a general tool for designing more efficient photoswitches and other functional molecules used in optoelectronic devices.

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  • 28.
    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 chemistry2003In: High Performance Computing for Computational Science — VECPAR 2002, Springer Berlin/Heidelberg, 2003, Vol. 2565, p. 137-165Conference paper (Refereed)
    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.

  • 29.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Computational Identification of Pyrrole Ring C as the Preferred Donor for Excited-State Proton Transfer in Bacteriophytochromes2018In: ChemPhotoChem, E-ISSN 2367-0932, Vol. 2, no 6, p. 453-457Article in journal (Refereed)
    Abstract [en]

    The engineering of bacteriophytochrome photoreceptors into near-infrared fluorescent proteins is a promising route toward deep-tissue imaging of living cells with many challenges ahead. One key objective is to increase the fluorescence quantum yields, which are limited by competing non-radiative relaxation processes involving not only the well-known double-bond photoisomerization of the tetrapyrrole chromophore, but also a potential excited-state proton transfer from the chromophore to the protein. Motivated by the lack of mechanistic knowledge about this proton transfer, we here use hybrid quantum mechanics/molecular mechanics methods to investigate three possible scenarios for how the process is initiated. Through calculated excited-state pKa values of the chromophore inside the protein matrix of Deinococcus radiodurans bacteriophytochrome, it is found that pyrrole ring C is a much more likely donor for excited-state proton transfer than rings A and B, which are also possible donors discussed in the literature. This finding offers a starting point for establishing a strategy to strengthen the fluorescence of engineered bacteriophytochromes through biochemical inhibition of the proton transfer.

  • 30.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Deciphering Excited-State Protonation and Tautomeric States of Oxyluciferin through Calculation of Excited-State Equilibrium Constants2013Manuscript (preprint) (Other academic)
    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.

  • 31.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 30, p. 2184-2194Article in journal (Refereed)
    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.

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  • 32.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Modeling of phytochrome absorption spectra2013In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 16, p. 1363-1374Article in journal (Refereed)
    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.

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  • 33.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome2015Manuscript (preprint) (Other academic)
    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.

  • 34.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study2013In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 19-28Article in journal (Refereed)
    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.

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  • 35.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Steric Effects Govern the Photoactivation of Phytochromes2016In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 17, no 7, p. 954-957Article in journal (Refereed)
    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.

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  • 36.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 49, p. 11911-11921Article in journal (Refereed)
    Abstract [en]

    Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states, can be supplemented by the ability to also describe inter-excited state phosphorescence. Specifically, 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.

  • 37.
    Fang, Changfeng
    et al.
    Center for Optics Research and Engineering, Shandong University.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Calculation of Free-Energy Barriers with TD-DFT: A Case Study on Excited-State Proton Transfer in Indigo2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 40, p. 8485-8495Article in journal (Refereed)
    Abstract [en]

    The performance of time-dependent density functional theory (TD-DFT) for the calculation of excited states of molecular systems has been the subject of many benchmark studies. Often, these studies focus on excitation energies or, more recently, excited-state equilibrium geometries. In this work, we take a different angle by instead exploring how well TD-DFT reproduces experimental free-energy barriers of a well-known photochemical reaction: the excited-state proton transfer (ESPT) in indigo. Specifically, by exploiting the possibility of using TD-DFT to locate and compute free energies of first-order saddle points in excited states, we test the performance of several popular density functionals in reproducing recently determined experimental free-energy barriers for ESPT in indigo and in an N-hexyl substituted derivative thereof. Through the calculations, it is found that all of the tested functionals perform quite well, uniformly overestimating the experimental values by 1.4–3.5 (mean error) and 2.5–5.5 kcal mol–1 (maximum error) only. Given that these errors are not larger than those typically observed when barriers for ground-state proton transfer reactions are calculated in ground-state DFT, the results highlight the potential of TD-DFT to enable accurate modeling of ESPT reactions based on free energies and explicit localization of transition states.

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  • 38.
    Fang, Changfeng
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Oruganti, Baswanth
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Computational study of the working mechanism and rate acceleration of overcrowded alkene-based light-driven rotary molecular motors2014In: RSC Advances, E-ISSN 2046-2069, Vol. 4, no 20, p. 10240-10251Article in journal (Refereed)
    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.

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  • 39.
    Fang, Changfeng
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Oruganti, Baswanth
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    How method-dependent are calculated differences between vertical, adiabatic, and 0-0 excitation energies?2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 23, p. 4157-4171Article in journal (Refereed)
    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.

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  • 40.
    Kalapos, Peter Pal
    et al.
    MTA TTK Lendulet Funct Organ Mat Res Grp, Hungary.
    Kunfi, Attila
    MTA TTK Lendulet Funct Organ Mat Res Grp, Hungary.
    Bogner, Marcell M.
    MTA TTK Lendulet Funct Organ Mat Res Grp, Hungary.
    Holczbauer, Tamas
    Res Ctr Nat Sci, Hungary.
    Kochman, Michal Andrzej
    Polish Acad Sci, Poland.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    London, Gabor
    MTA TTK Lendulet Funct Organ Mat Res Grp, Hungary.
    Salicylideneaniline/Dithienylethene Hybrid Molecular Switches: Design, Synthesis, and Photochromism2023In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 89, no 1, p. 16-26Article in journal (Refereed)
    Abstract [en]

    A hybrid molecular switch comprising salicylideneaniline (SA) and dithienylethene (DTE) moieties around a single benzene ring is reported. Due to an interplay between solvent-assisted enol-keto tautomerization in the former moiety and photochromic electrocyclization in the latter, this dithienylbenzene derivative was found to be photoresponsive at room temperature with a thermally stable closed form. The main photoproduct featuring ring-closed DTE and keto-enamine SA structures could be isolated and converted back to the starting material by irradiation with visible light. The optical properties of the potential structures involved in the overall process were characterized by using density functional theory (DFT) calculations in good agreement with the measured data. The reversibility of the conversion could be tuned by the presence of donor and acceptor substituents, while the introduction of the imine in the form of a benzothiazole moiety enabled photochemistry even in nonprotic solvents.

  • 41.
    Kalapos, Peter Pal
    et al.
    Res Ctr Nat Sci, Hungary.
    Mayer, Peter J.
    Res Ctr Nat Sci, Hungary; Univ Szeged, Hungary.
    Gazdag, Tamas
    Res Ctr Nat Sci, Hungary; Eotvos Lorand Univ, Hungary.
    Demeter, Attila
    Res Ctr Nat Sci, Hungary.
    Oruganti, Baswanth
    Linnaeus Univ, Sweden.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    London, Gabor
    Res Ctr Nat Sci, Hungary.
    Photoswitching of Local (Anti)Aromaticity in Biphenylene-Based Diarylethene Molecular Switches2022In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 87, no 15, p. 9532-9542Article in journal (Refereed)
    Abstract [en]

    Photoinduced tuning of (anti)aromaticity and associated molecular properties is currently in the focus of attention for both tailoring photochemical reactivity and designing new materials. Here, we report on the synthesis and spectroscopic characterization of diarylethene-based molecular switches embedded in a biphenylene structure composed of rings with different levels of local (anti)aromaticity. We show that it is possible to modulate and control the (anti)aromatic character of each ring through reversible photoswitching of the aryl units of the system between open and closed forms. Remarkably, it is shown that the irreversible formation of an annulated bis(dihydro-thiopyran) side-product that hampers the photoswitching can be efficiently suppressed when the aryl core formed by thienyl groups in one switch is replaced by thiazolyl groups in another.

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  • 42.
    Kochman, Michal Andrzej
    et al.
    Polish Acad Sci, Poland.
    Gryber, Tomasz
    Polish Acad Sci, Poland.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Kubas, Adam
    Polish Acad Sci, Poland.
    Simulation and analysis of the relaxation dynamics of a photochromic furylfulgide2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 30, p. 18103-18118Article in journal (Refereed)
    Abstract [en]

    Furylfulgides, a class of photochromic organic compounds, show a complex system of photoinduced reactions. In the present study, the excited-state dynamics of the E-alpha and E-beta isomers of a representative furylfulgide is modelled with the use of nonadiabatic molecular dynamics simulations. Moreover, a pattern recognition algorithm is employed in order to automatically identify relaxation pathways, and to quantify the photoproduct distributions. The simulation results indicate that, despite differing only in the orientation of the furyl group, the two isomers show markedly different photochemical behaviour. The predominant E-alpha isomer undergoes photocyclisation with a quantum yield (QY) of 0.27 +/- 0.10. For this isomer, the undesired E -&gt; Z photoisomerisation around the central double bond represents a minor side reaction, with a QY of 0.09 +/- 0.07. In contrast, the minority E-beta isomer, which is incapable of photocyclisation, undergoes efficient E -&gt; Z photoisomerisation, with a QY as high as 0.56 +/- 0.14. The relaxation kinetics and the photoproduct distributions are interpreted in the light of the available experimental data.

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  • 43.
    Kochman, Michal
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Simulating the Nonadiabatic Relaxation Dynamics of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Polar Solution2020In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 124, no 11, p. 2193-2206Article in journal (Refereed)
    Abstract [en]

    The compound 4-(N,N-dimethylamino)-benzonitrile (DMABN) represents the archetypal system for dual fluorescence, a rare photophysical phenomenon in which a given fluorophore shows two distinct emission bands. Despite extensive studies, the underlying mechanism remains the subject of debate. In the present contribution, we address this issue by simulating the excited-state relaxation process of DMABN as it occurs in polar solution. The potential energy surfaces for the system are constructed with the use of the additive quantum mechanics/molecular mechanism (QM/MM) method, and the coupled dynamics of the electronic wave function and the nuclei is propagated with the semiclassical fewest switches surface hopping method. The DMABN molecule, which comprises the QM subsystem, is treated with the use of the second-order algebraic diagrammatic construction (ADC(2)) method with the imposition of spin-opposite scaling (SOS). It is verified that this level of theory achieves a realistic description of the excited-state potential energy surfaces of DMABN. The simulation results qualitatively reproduce the main features of the experimentally observed fluorescence spectrum, thus allowing the unambiguous assignment of the two fluorescence bands: the normal band is due to the near-planar locally excited (LE) structure of DMABN, while the so-called "anomalous" second band arises from the twisted intramolecular charge transfer (TICT) structure. The transformation of the LE structure into the TICT structure takes place directly via intramolecular rotation, and is not mediated by another excited-state structure. In particular, the oft-discussed rehybridized intramolecular charge transfer (RICT) structure, which is characterized by a bent nitrile group, does not play a role in the relaxation process.  

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  • 44.
    Kochman, Michal
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Theoretical Study of Ground- and Excited-State Charge Transfer in Fulvene-Based Donor-Acceptor Systems2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 31, p. 6660-6673Article in journal (Refereed)
    Abstract [en]

    Donor-acceptor systems based on fulvene as the electron-accepting moiety are typified by exotic, strongly polar electronic structures. In this contribution, ab initio calculations have been performed to explore the ground- and excited-state properties of an archetypal compound of this class, which incorporates the exocyclic carbon atom of fulvene into a tetramethylimidazoline-like five-membered ring. In the electronic ground state, the compound under study has a pronounced zwitterionic character and is best described as consisting of a negatively charged cyclopentadienyl ring linked covalently to a positively charged tetramethylimidazolium ring. Both of these rings can be considered as aromatic. The excess negative charge localized on the cyclopentadienyl ring is highly labile in the photochemical sense: the low-lying valence excited states exhibit varying degrees of reverse charge transfer, whereby electron density is transferred from the cyclopentadienyl ring back onto the tetramethylimidazolium ring. The topographies of the excited-state potential energy surfaces favor rapid and efficient internal conversion at an extended, fulvene-like S1/S0 conical intersection seam. As a consequence, the excited-state lifetime of this compound is predicted to be on the order of 100 fs. 

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  • 45.
    Kochman, Michał Andrzej
    et al.
    Polish Academy of Sciences, Poland.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Kubas, Adam
    Polish Academy of Sciences, Poland.
    Simulation and Analysis of the Transient Absorption Spectrum of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Acetonitrile2021In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 125, no 39, p. 8635-8648Article in journal (Refereed)
    Abstract [en]

    4-(N,N-Dimethylamino)benzonitrile (DMABN) is a well-known model compound for dual fluorescence ﹣in sufficiently polar solvents, it exhibits two distinct fluorescence emission bands. The interpretation of its transient absorption (TA) spectrum in the visible range is the subject of a long-standing controversy. In the present study, we resolve this issue by calculating the TA spectrum on the basis of nonadiabatic molecular dynamics simulations. An unambiguous assignment of spectral signals to specific excited-state structures is achieved by breaking down the calculated spectrum into contributions from twisted and nontwisted molecular geometries. In particular, the much-discussed excited-state absorption band near 1.7 eV (ca. 700nm) is attributed to the near-planar locally excited (LE) minimum on the S1 state. On the technical side, our study demonstrates that the second-order approximate coupled cluster singles and doubles (CC2) method can be used successfully to calculate the TA spectra of moderately large organic molecules, provided that the system in question does not approach a crossing between the lowest excited state and the singlet ground state within the time frame of the simulation.

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  • 46.
    Lv, Jiezhao
    et al.
    Shandong Univ, Peoples R China.
    Fang, Changfeng
    Shandong Univ, Peoples R China.
    Zhu, Chengjie
    Soochow Univ, Peoples R China.
    Sun, Peng
    Shandong Univ, Peoples R China.
    Li, Yvonne Y.
    Harvard Med Sch, MA 02215 USA.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Zhao, Xian
    Shandong Univ, Peoples R China.
    Deng, Lu
    Shandong Univ, Peoples R China.
    Numerical Investigation of the Stimulated Growth of Single-Crystal Fibers by Point-Effect-Induced Fluid Dynamics2022In: Crystal Growth & Design, ISSN 1528-7483, E-ISSN 1528-7505, Vol. 22, no 12, p. 7031-7039Article in journal (Refereed)
    Abstract [en]

    Using molecular dynamics analysis and a two-component diffusion model that accounts for the time-dependent crystal surface chemical reaction, we show by extensive numerical simulations that the recently observed prismatic facet growth suppression in single-crystal fibers is the combined action of self-shielding by crystal surface selectivity and self-channeling arising from a point effect due to fibers small diameters and large aspect ratios. We further show that the self-channeling leads to a pyramidal-face-aiming solute flow, resulting in accelerated single-crystal fiber growth. This mesoscopic stimulated matter growth acceleration theory can satisfactorily explain all experimental results reported to date. This new crystal fiber growth technology opens a realm of application possibilities for single-crystal fiber architectures in chip-size photonics.

  • 47.
    Oruganti, Baswanth
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents2016In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 22, no 9, p. 219-Article in journal (Refereed)
    Abstract [en]

    We employ computational methods to investigate the possibility of using electron-donating or electron-withdrawing substituents to reduce the free-energy barriers of the thermal isomerizations that limit the rotational frequencies achievable by synthetic overcrowded alkene-based molecular motors. Choosing as reference systems one of the fastest motors known to date and two variants thereof, we consider six new motors obtained by introducing electron-donating methoxy and dimethylamino or electron-withdrawing nitro and cyano substituents in conjugation with the central olefinic bond connecting the two (stator and rotator) motor halves. Performing density functional theory calculations, we then show that electron-donating (but not electron-withdrawing) groups at the stator are able to reduce the already small barriers of the reference motors by up to 18 kJ mol(-1). This result outlines a possible strategy for improving the rotational frequencies of motors of this kind. Furthermore, exploring the origin of the catalytic effect, it is found that electron-donating groups exert a favorable steric influence on the thermal isomerizations, which is not manifested by electron-withdrawing groups. This finding suggests a new mechanism for controlling the critical steric interactions of these motors.

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  • 48.
    Oruganti, Baswanth
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Fang, Changfeng
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Assessment of a composite CC2/DFT procedure for calculating 0-€“0 excitation energies of organic molecules2016In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 114, no 23, p. 3448-3463Article in journal (Refereed)
    Abstract [en]

    The task to assess the performance of quantum chemical methods in describing electronically excited states has in recent years started to shift from calculation of vertical (ΔEve) to calculation of 0-€“0 excitation energies (ΔE00). Here, based on a set of 66 excited states of organic molecules for which high-resolution experimental ΔE00 energies are available and for which the approximate coupled-cluster singles and doubles (CC2) method performs particularly well, we explore the possibility to simplify the calculation of CC2-quality ΔE00 energies using composite procedures that partly replace CC2 with more economical methods. Specifically, we consider procedures that employ CC2 only for the ΔEve part and density functional theory methods for the cumbersome excited-state geometry optimisations and frequency calculations required to obtain ΔE00 energies from ΔEve ones. The results demonstrate that it is indeed possible to both closely (to within 0.06-€“0.08 eV) and consistently approximate ‘true’ CC2 ΔE00 energies in this way, especially when CC2 is combined with hybrid density functionals. Overall, the study highlights the unexploited potential of composite procedures, which hitherto have found widespread use mostly in ground-state chemistry, to also play an important role in facilitating accurate studies of excited states.

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  • 49.
    Oruganti, Baswanth
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Fang, Changfeng
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering. Jining University, Peoples R China.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 33, p. 21740-21751Article in journal (Refereed)
    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.

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  • 50.
    Oruganti, Baswanth
    et al.
    ‎ Linnaeus Univ, Fac Hlth & Life Sci, Dept Chem & Biomed Sci, SE-45041 Kalmar, Sweden.
    Kalapos, Péter Pál
    Res Ctr Nat Sci, Inst Organ Chem, MTA TTK Lendulet Funct Organ Mat Res Grp, H-1117 Budapest, Hungary.
    Bhargav, Varada
    GITAM Deemed Be Univ, GITAM Inst Sci, Dept Chem, Visakhapatnam 530045, Andhra Pradesh, India.
    London, Gábor
    Res Ctr Nat Sci, Inst Organ Chem, MTA TTK Lendulet Funct Organ Mat Res Grp, H-1117 Budapest, Hungary.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Photoinduced Changes in Aromaticity Facilitate Electrocyclization of Dithienylbenzene Switches2020In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 142, no 32, p. 13941-13953Article in journal (Refereed)
    Abstract [en]

    The concepts of excited-state aromaticity and antiaromaticity have in recent years with increasing frequency been invoked to rationalize the photochemistry of cyclic conjugated organic compounds, with the long-term goal of using these concepts to improve the reactivities of such compounds toward different photochemical transformations. In this regard, it is of particular interest to assess how the presence of a benzene motif affects photochemical reactivity, as benzene is well-known to completely change its aromatic character in its lowest excited states. Here, we investigate how a benzene motif influences the photoinduced electrocyclization of dithienylethenes, a major class of molecular switches. Specifically, we report on the synthesis of a dithienylbenzene switch where the typical nonaromatic, ethene-like motif bridging the two thienyl units is replaced by a benzene motif, and show that this compound undergoes electrocyclization upon irradiation with UV-light. Furthermore, through a detailed quantum chemical analysis, we demonstrate that the electrocyclization is driven jointly and synergistically by the loss of aromaticity in this motif from the formation of a reactive, antiaromatic excited state during the initial photoexcitation, and by the subsequent relief of this antiaromaticity as the reaction progresses from the Franck-Condon region. Overall, we conclude that photoinduced changes in aromaticity facilitate the electrocyclization of dithienylbenzene switches. 

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