| 1. |
- Arpa González, Enrique Manuel, 1991-, et al.
(författare)
-
In Silico Design of Dihydroazulene/Vinylheptafulvene Photoswitches for Solar-Energy Storage Guided by an All-Around Performance Descriptor
- 2023
-
Ingår i: Chemistry−Methods. - Weinheim, Germany : Wiley-VCH Verlagsgesellschaft. - 2628-9725. ; 3
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 2. |
- Arpa González, Enrique Manuel, et al.
(författare)
-
Transient changes in aromaticity and their effect on excited-state proton transfer reactions
- 2022
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:19, s. 11496-11500
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 3. |
- Durbeej, Bo, 1973-
(författare)
-
A computational perspective on the photochemistry of photosensory proteins : phytochromes and Anabaena sensory rhodopsin
- 2012
-
Ingår i: Quantum Simulations of Materials and Biological Systems. - Dordrecht : Springer Netherlands. - 9789400749474 ; , s. 169-194
-
Bokkapitel (refereegranskat)abstract
- 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.
|
|
| 4. |
- Durbeej, Bo, Professor, 1973-
(författare)
-
Competing Excited-State Deactivation Processes in Bacteriophytochromes
- 2020
-
Ingår i: Chemical Physics and Quantum Chemistry. - : Elsevier. - 9780128197578 ; , s. 243-268
-
Bokkapitel (refereegranskat)abstract
- 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.
|
|
| 5. |
- Durbeej, Bo, 1973-, et al.
(författare)
-
Molecular Photoswitching Aided by Excited-State Aromaticity
- 2018
-
Ingår i: ChemPlusChem. - Weinheim, Germany : Wiley-VCH Verlagsgesellschaft. - 2192-6506. ; 83:11, s. 958-967
-
Tidskriftsartikel (refereegranskat)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/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.
|
|
| 6. |
- Durbeej, Bo, 1973-
(författare)
-
Quantum Chemical Studies of Protein-Bound Chromophores, UV-Light Induced DNA Damages, and Lignin Formation
- 2004
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin. The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed. DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.
|
|
| 7. |
- Falklöf, Olle, 1986-, et al.
(författare)
-
Computational Identification of Pyrrole Ring C as the Preferred Donor for Excited-State Proton Transfer in Bacteriophytochromes
- 2018
-
Ingår i: ChemPhotoChem. - Weinheim, Germany : Wiley-VCH Verlagsgesellschaft. - 2367-0932. ; 2:6, s. 453-457
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 8. |
- Fang, Changfeng, et al.
(författare)
-
Calculation of Free-Energy Barriers with TD-DFT: A Case Study on Excited-State Proton Transfer in Indigo
- 2019
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 123:40, s. 8485-8495
-
Tidskriftsartikel (refereegranskat)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 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.
|
|
| 9. |
- Kochman, Michał Andrzej, et al.
(författare)
-
Simulation and Analysis of the Transient Absorption Spectrum of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Acetonitrile
- 2021
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:39, s. 8635-8648
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 10. |
- Kochman, Michal, 1987-, et al.
(författare)
-
Simulating the Nonadiabatic Relaxation Dynamics of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Polar Solution
- 2020
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 124:11, s. 2193-2206
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
