ORCID Profile
0000-0001-5847-1196
Current Organisation
Linköping University
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Publisher: Royal Society of Chemistry (RSC)
Date: 2017
DOI: 10.1039/C6CP08484B
Abstract: Despite lacking a stereocenter, light-driven cyclohexenylidene-pyrrolinium molecular motors achieve unidirectional rotary motion through the asymmetry afforded by the puckered cyclohexenylidene.
Publisher: Royal Society of Chemistry (RSC)
Date: 2004
DOI: 10.1039/B411005F
Publisher: Springer Netherlands
Date: 2012
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C4CP06124A
Abstract: We present evidence that astaxanthin enolate may form in a protein complex environment, and is associated with a large bathochromic absorption shift to give the blue–black color of lobsters.
Publisher: Walter de Gruyter GmbH
Date: 08-01-2003
DOI: 10.1515/HF.2003.009
Publisher: American Society for Photobiology
Date: 05-2007
Publisher: Wiley
Date: 02-2023
Abstract: 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.
Publisher: Informa UK Limited
Date: 30-09-2016
Publisher: Elsevier
Date: 2020
Publisher: Wiley
Date: 2003
DOI: 10.1562/0031-8655(2003)078<0159:OTFOCP>2.0.CO;2
Abstract: 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 x T), cytosine + cytosine (C + C --> C x C) and cytosine + thymine (C + T --> C x 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 x 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.
Publisher: Royal Society of Chemistry (RSC)
Date: 2006
DOI: 10.1039/B605682B
Abstract: 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.
Publisher: Elsevier BV
Date: 06-2003
Publisher: Elsevier BV
Date: 11-2013
Publisher: American Chemical Society (ACS)
Date: 30-03-2021
Publisher: Wiley
Date: 19-08-2009
Abstract: The degree to which the corrin ring portion of coenzyme B 12 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 B 12 . 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 (TS B CorIm). In the TS complex where the ribose instead is positioned in orientation A, no such effect is manifested. The observed stabilization in TS B CorIm appears to be the result of favorable interactions involving O3′ and the corrin ring, including a CH⋅⋅⋅O hydrogen bond. We find that the degree of stabilization is not particularly sensitive to the CoC distance. Our calculations show that any potential stabilization afforded to the H‐atom‐abstraction step by coenzyme B 12 is sensitive to the orientation of the ribose moiety.
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D2CP02143A
Abstract: The complex photochemistry of a model furylfulgide is resolved with a combination of nonadiabatic molecular simulations and pattern recognition analysis of molecular geometry.
Publisher: American Chemical Society (ACS)
Date: 15-07-2020
DOI: 10.1021/JACS.0C06327
Publisher: Wiley
Date: 16-09-2014
DOI: 10.1002/JCC.23735
Abstract: 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 (OxyLH2) 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 OxyLH2. Particularly, rather than relying on the standard Förster 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 OxyLH2 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 OxyLH2 in the excited state, which suggests a potential key role for this species in the bioluminescence of fireflies.
Publisher: Elsevier BV
Date: 2019
Publisher: American Chemical Society (ACS)
Date: 21-08-2020
Publisher: Springer Science and Business Media LLC
Date: 24-08-2016
Publisher: American Chemical Society (ACS)
Date: 10-2000
DOI: 10.1021/JA000929J
Publisher: Elsevier BV
Date: 11-2005
Publisher: Springer Science and Business Media LLC
Date: 04-2011
DOI: 10.1039/C0PP00307G
Abstract: 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.
Publisher: Elsevier BV
Date: 09-2002
Publisher: American Chemical Society (ACS)
Date: 11-07-2020
Abstract: 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 S
Publisher: American Chemical Society (ACS)
Date: 23-08-2022
Publisher: Royal Society of Chemistry (RSC)
Date: 2022
DOI: 10.1039/D2CP00494A
Abstract: Quantum chemical modelling shows that energy barriers for excited-state proton transfer reactions involving 2-pyridone are governed by the transient onset of antiaromaticity upon interaction between the photoexcited state and a second excited state.
Publisher: American Chemical Society (ACS)
Date: 25-11-2015
Abstract: Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states can be supplemented by the ability to also describe inter-excited-state phosphorescence. Specifically, by performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing (1)(πHπL*) singlet state of lumiflavin to the (3)(πHπL*), (3)(nN2πL*), and (3)(πH-1πL*) triplet states, and subsequently, we compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically 2 to 5 orders of magnitude smaller than the nonradiative ones.
Publisher: American Chemical Society (ACS)
Date: 25-08-2017
DOI: 10.1021/ACS.ORGLETT.7B02257
Abstract: A new approach to the design of more efficient light-driven rotary molecular motors is presented and evaluated computationally based on molecular dynamics simulations. The approach involves enabling part of the motor to become aromatic in the photoactive excited state, and is found to sharply increase the rotary quantum yields of the photoisomerizations that underlie the motor function. Excited-state aromaticity thus holds promise as a guiding principle toward better-performing molecular motors.
Publisher: American Chemical Society (ACS)
Date: 03-2007
DOI: 10.1021/JP0676383
Abstract: 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.
Publisher: American Chemical Society (ACS)
Date: 07-03-2018
DOI: 10.1021/JP050873L
Abstract: 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.
Publisher: American Chemical Society (ACS)
Date: 07-11-2022
Publisher: Wiley
Date: 31-10-2023
Publisher: Wiley
Date: 28-02-2019
Publisher: American Chemical Society (ACS)
Date: 23-02-2013
DOI: 10.26434/CHEMRXIV-2023-CZSF4
Abstract: 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 parameterized for excited states. Against this background, we here present a new parameterization of HOMA − termed HOMER − for the T1 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.
Publisher: Wiley
Date: 28-05-2012
DOI: 10.1002/JCC.23027
Abstract: 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 S(1) 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.
Publisher: American Chemical Society (ACS)
Date: 11-09-2007
DOI: 10.1021/JP0727953
Abstract: 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.
Publisher: Royal Society of Chemistry (RSC)
Date: 2023
DOI: 10.1039/D3CP00842H
Abstract: A geometric model to probe excited-state aromaticity and antiaromaticity termed HOMER is reported. When tested by quantum-chemical calculations on carbocyclic and heterocyclic systems, the model is found consistent with state-of-the-art magnetic data.
Publisher: Proceedings of the National Academy of Sciences
Date: 22-11-2010
Abstract: 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° 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°) unidirectional rotation of the ═C14─C15═ moiety. This finding implies that Anabaena sensory rhodopsin is a biological realization of a light-driven molecular rotor.
Publisher: American Chemical Society (ACS)
Date: 04-07-2023
DOI: 10.26434/CHEMRXIV-2023-9362L
Abstract: 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 single-bond axis is a formidable challenge in the field of artificial molecular machines. Here, we present a new design of such photogears that is based on the possibility to use stereogenic substituents to control both the relative stabilities of the two helical forms of the photogear and the double-bond photoisomerization that connects them. The potential of the design is verified by quantum-chemical modeling through which photogearing is 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.
Publisher: Wiley
Date: 04-11-2016
Publisher: Royal Society of Chemistry (RSC)
Date: 2004
DOI: 10.1039/B404431B
Publisher: Walter de Gruyter GmbH
Date: 20-08-2003
DOI: 10.1515/HF.2003.070
Abstract: 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.
Publisher: American Chemical Society (ACS)
Date: 12-09-2019
Abstract: 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
Publisher: Wiley
Date: 23-04-2020
DOI: 10.1002/JCC.26213
Publisher: Wiley
Date: 03-2013
DOI: 10.1002/JCC.23265
Abstract: 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.
Publisher: American Chemical Society (ACS)
Date: 21-02-2020
Publisher: Wiley
Date: 04-03-2016
Publisher: Wiley
Date: 30-08-2018
Abstract: 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 roton 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.
Publisher: Wiley
Date: 16-12-2022
DOI: 10.1002/POC.4468
Publisher: American Chemical Society (ACS)
Date: 22-09-2021
Publisher: American Chemical Society (ACS)
Date: 03-06-2014
DOI: 10.1021/JP501974P
Abstract: 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.
Publisher: Royal Society of Chemistry (RSC)
Date: 2009
DOI: 10.1039/B811813B
Abstract: 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 an accuracy of approximately 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 in the 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.
Publisher: Wiley
Date: 30-03-2018
Publisher: Wiley
Date: 08-10-2018
Abstract: 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.
Publisher: American Chemical Society (ACS)
Date: 24-03-2009
DOI: 10.1021/JP810754S
Abstract: 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.
Publisher: American Chemical Society (ACS)
Date: 18-07-2022
Publisher: Wiley
Date: 08-2018
Publisher: Wiley
Date: 22-10-2021
Abstract: A popular approach to the calculation of molecular excitation energies is to consider only equilibrium geometries and neglect the effects of thermal motion. Although this static approach is sensible for molecules with distinct potential‐energy minima, its adequacy relative to dynamical approaches appears not to have been thoroughly tested. Here, we report a case study investigating how thermal motion accounted for by molecular dynamics simulations influences the optically bright state of astaxanthin, a carotenoid of broad photobiological interest that features 13 conjugated double bonds. Employing several different density functional methods, it is shown that thermal fluctuations in the conjugation result in the Boltzmann‐weighted average excitation energies for this state being shifted by up to 0.05 eV relative to those obtained from purely static calculations. Accordingly, it is concluded that the effects of thermal motion on excitation energies of conjugated systems can be quite large even for molecules with distinct potential‐energy minima.
Publisher: Walter de Gruyter GmbH
Date: 27-02-2003
DOI: 10.1515/HF.2003.024
Abstract: 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.
Publisher: Royal Society of Chemistry (RSC)
Date: 2008
DOI: 10.1039/B719190A
Abstract: 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) pKa s 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 pKa s 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.
Publisher: Royal Society of Chemistry (RSC)
Date: 2015
DOI: 10.1039/C5CP02303C
Abstract: By tuning the steric bulkiness of the stereogenic substituent, the rate-determining thermal free-energy barrier of an already MHz-capable rotary molecular motor can be reduced by a further 15–17 kJ mol −1 .
Publisher: American Chemical Society (ACS)
Date: 19-09-2022
DOI: 10.26434/CHEMRXIV-2022-ZJSRB
Abstract: The possibility to use the reversible cycling of molecular photoswitches between isomeric forms as a means to store and release solar energy has stimulated the development of candidate systems based on several different core structures, such as the dihydroazulene/vinylheptafulvene (DHA/VHF) couple. However, a major challenge in these efforts is to simultaneously realize many of the performance criteria required of the switches for such applications. Here, we take on this challenge by first introducing an all-around performance descriptor that combines three key criteria (related to energy density, storage time and light-absorption characteristics), and by then using density functional theory (DFT) methods to calculate its values for 52 newly designed DHA/VHF switches. Through this approach, we are able to identify several switches with excellent overall properties that contain a structural motif absent in all DHA/VHF compounds considered for solar-energy storage in the existing literature. For some of these switches, we also provide retrosynthetic analyses for their preparation and perform DFT calculations to 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.
Publisher: Wiley
Date: 31-08-2016
Abstract: Synthetic overcrowded alkene-based molecular motors achieve 360° unidirectional rotary motion of one motor half (rotator) relative to the other (stator) through sequential photochemical and thermal isomerisation steps. In order to facilitate and expand the use of these motors for various applications, it is important to investigate ways to increase the rates and efficiencies of the reactions governing the rotary motion. Here, we use computational methods to explore whether the thermal isomerisation performance of some of the fastest available motors of this type can be further improved by reducing the sizes of the motor halves. Presenting three new redesigned motors that combine an indanylidene rotator with a cyclohexadiene, pyran or thiopyran stator, we first use multiconfigurational quantum chemical methods to verify that the photoisomerisations of these motors sustain unidirectional rotary motion. Then, by performing density functional calculations, we identify both stepwise and concerted mechanisms for the thermal isomerisations of the motors and show that the rate-determining free-energy barriers of these processes are up to 25 kJ mol
Publisher: Royal Society of Chemistry (RSC)
Date: 2014
DOI: 10.1039/C3RA46880A
Publisher: American Chemical Society (ACS)
Date: 06-01-2012
DOI: 10.1021/JA207809B
Abstract: Vitamin B(12) and its biologically active counterparts possess the only ex les 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 B(12) (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(•)) 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 that help understand how B(12) enzymes catalyze coenzyme activation and control highly reactive radical intermediates.
Publisher: Wiley
Date: 20-01-2016
Abstract: 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 Z→E 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.
Publisher: Wiley
Date: 12-05-2017
DOI: 10.1002/QUA.25405
No related grants have been discovered for Bo Durbeej.