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Durbeej, Bo
Publications (10 of 38) Show all publications
Wang, J., Oruganti, B. & Durbeej, B. (2019). A Straightforward Route to Aromatic Excited States in Molecular Motors that Improves Photochemical Efficiency. ChemPhotoChem, 3(6), 450-460
Open this publication in new window or tab >>A Straightforward Route to Aromatic Excited States in Molecular Motors that Improves Photochemical Efficiency
2019 (English)In: ChemPhotoChem, ISSN 2367-0932, Vol. 3, no 6, p. 450-460Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
Weinheim, Germany: Wiley-VCH Verlagsgesellschaft, 2019
Keywords
Aromaticity, Donor-acceptor systems, Molecular devices, Molecular dynamics, Quantum yields
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-156236 (URN)10.1002/cptc.201800268 (DOI)000471720500023 ()
Funder
Swedish Research Council, 621-2011-4353Stiftelsen Olle Engkvist Byggmästare, 2014/734 and 184-568
Note

Funding agencies:  Swedish Research Council [621-2011-4353]; Olle Engkvist Foundation [2014/734, 184-568]; Linkoping University

Available from: 2019-04-08 Created: 2019-04-08 Last updated: 2019-07-18Bibliographically approved
Zhang, J., Wang, J., Sandberg, A., Wu, X., Nyström, S., LeVine, H. I., . . . Lindgren, M. (2018). Intramolecular Proton and Charge Transfer of Pyrene-based trans-Stilbene Salicylic Acids Applied to Detection of Aggregated Proteins.. ChemPhysChem, 19(22), 3001-3009
Open this publication in new window or tab >>Intramolecular Proton and Charge Transfer of Pyrene-based trans-Stilbene Salicylic Acids Applied to Detection of Aggregated Proteins.
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2018 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, no 22, p. 3001-3009Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
Weinheim, Germany: Wiley-VCH Verlag, 2018
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-152767 (URN)10.1002/cphc.201800823 (DOI)000450672100006 ()30183138 (PubMedID)
Available from: 2018-11-20 Created: 2018-11-20 Last updated: 2018-12-10
Wang, J. & Durbeej, B. (2018). Toward Fast and Efficient Visible-Light-Driven Molecular Motors: A Minimal Design. ChemistryOpen, 7(8), 583-589
Open this publication in new window or tab >>Toward Fast and Efficient Visible-Light-Driven Molecular Motors: A Minimal Design
2018 (English)In: ChemistryOpen, ISSN 2191-1363, Vol. 7, no 8, p. 583-589Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
Weinheim, Germany: Wiley-VCH Verlagsgesellschaft, 2018
Keywords
isomerization, molecular devices, molecular dynamics, quantum chemistry, visible light
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-149914 (URN)10.1002/open.201800089 (DOI)30083493 (PubMedID)
Funder
Swedish Research Council, 621-2011-4353Stiftelsen Olle Engkvist Byggmästare, 2014/734 and 184-568Carl Tryggers foundation , CTS 15:134Linköpings universitet
Note

Funding agencies: Swedish Research Council [621-2011-4353]; Olle Engkvist Foundation [2014/734, 184-568]; Carl Trygger Foundation [CTS 15:134]; Linkoping University

Available from: 2018-08-03 Created: 2018-08-03 Last updated: 2018-09-13
Falklöf, O. & Durbeej, B. (2016). Steric Effects Govern the Photoactivation of Phytochromes. ChemPhysChem, 17(7), 954-957
Open this publication in new window or tab >>Steric Effects Govern the Photoactivation of Phytochromes
2016 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 17, no 7, p. 954-957Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2016
Keywords
chromophores; isomerization; photoreceptor proteins; QM; MM modeling; range-separated functionals
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-127554 (URN)10.1002/cphc.201501080 (DOI)000373738200002 ()26756452 (PubMedID)
Note

Funding Agencies|Linkoping University; Swedish Research Council [621-2011-4353]; Olle Engkvist Foundation

Available from: 2016-05-04 Created: 2016-05-03 Last updated: 2017-11-30
Oruganti, B., Fang, C. & Durbeej, B. (2015). Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects. Physical Chemistry, Chemical Physics - PCCP, 17(33), 21740-21751
Open this publication in new window or tab >>Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects
2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 33, p. 21740-21751Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2015
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-121153 (URN)10.1039/c5cp02303c (DOI)000359596600080 ()26234787 (PubMedID)
Note

Funding Agencies|Linkoping University; Swedish Research Council; Olle Engkvist Foundation; Wenner-Gren Foundations; NSFC [11404141]; National Supercomputer Centre (NSC) in Linkoping

Available from: 2015-09-08 Created: 2015-09-08 Last updated: 2018-03-22
Falklöf, O., Durbeej, B. & Norman, P. (2015). Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin. Journal of Physical Chemistry A, 119(49), 11911-11921
Open this publication in new window or tab >>Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin
2015 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 49, p. 11911-11921Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2015
Keywords
Inter-excited state transition dipole moments, Radiative transitions, Nonradiative transitions, Response theory, Time-dependent density functional theory, Flavin chromophores
National Category
Chemical Sciences Physical Chemistry
Identifiers
urn:nbn:se:liu:diva-122743 (URN)10.1021/acs.jpca.5b08908 (DOI)000366339400016 ()
Note

Vid tiden för disputation förelåg publikationen som manuskript

Available from: 2015-11-19 Created: 2015-11-19 Last updated: 2017-12-01Bibliographically approved
Begum, S., Cianci, M., Durbeej, B., Falklöf, O., Haedener, A., Helliwell, J. R., . . . Watt, I. F. (2015). On the origin and variation of colors in lobster carapace. Physical Chemistry, Chemical Physics - PCCP, 17(26), 16723-16732
Open this publication in new window or tab >>On the origin and variation of colors in lobster carapace
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2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 26, p. 16723-16732Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2015
National Category
Chemical Sciences
Identifiers
urn:nbn:se:liu:diva-120247 (URN)10.1039/c4cp06124a (DOI)000356874000010 ()25797168 (PubMedID)
Note

Funding Agencies|Bildungs- und Kultur-departement des Kantons Luzern, Switzerland; Swedish Research Council; Olle Engkvist Foundation; Nuffield Foundation; School of Chemistry, University of Manchester; European Molecular Biology Laboratory

Available from: 2015-07-21 Created: 2015-07-20 Last updated: 2017-12-04
Falklöf, O. & Durbeej, B. (2015). QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome.
Open this publication in new window or tab >>QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome
2015 (English)Manuscript (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.

National Category
Chemical Sciences Physical Chemistry
Identifiers
urn:nbn:se:liu:diva-122744 (URN)
Available from: 2015-11-19 Created: 2015-11-19 Last updated: 2015-11-26Bibliographically approved
Fang, C., Oruganti, B. & Durbeej, B. (2014). Computational study of the working mechanism and rate acceleration of overcrowded alkene-based light-driven rotary molecular motors. RSC Advances, 4(20), 10240-10251
Open this publication in new window or tab >>Computational study of the working mechanism and rate acceleration of overcrowded alkene-based light-driven rotary molecular motors
2014 (English)In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 4, no 20, p. 10240-10251Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2014
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-104688 (URN)10.1039/C3RA46880A (DOI)000332061300048 ()2-s2.0-84894247198 (Scopus ID)
Available from: 2014-02-22 Created: 2014-02-22 Last updated: 2017-12-05Bibliographically approved
Falklöf, O. & Durbeej, B. (2014). Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants. Journal of Computational Chemistry, 35(30), 2184-2194
Open this publication in new window or tab >>Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants
2014 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 30, p. 2184-2194Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Wiley: 12 months, 2014
Keywords
light emission; tautomerism; protonation state; Born-Haber cycle; density functional theory
National Category
Physical Sciences
Identifiers
urn:nbn:se:liu:diva-112610 (URN)10.1002/jcc.23735 (DOI)000344173700003 ()25226816 (PubMedID)
Note

Funding Agencies|Linkoping University; Swedish Research Council; Olle Engkvist Foundation; Wenner-Gren Foundations

Available from: 2014-12-10 Created: 2014-12-05 Last updated: 2017-12-05
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