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Excited Electronic States of Organic Molecules–50 Years of an Interdisciplinary Research —A Tribute to Sir George Porter on the Occasion of His 100th Birthday

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 14229

Special Issue Editors

Dr. Dieter Leupold

E-Mail
Guest Editor
LTB Lasertechnik Berlin GmbH, 12489 Berlin, Germany
Interests: biomolecules; pi-electronic systems; melanin; melanomagenesis; laser spectroscopy; fluorescence diagnostics of tumors
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Hugo Scheer

E-Mail Website
Guest Editor
Ludwig-Maximilians-University (retired), Munich, Germany
Interests: photobiolgy; photosynthesis; photosensitization; tetrapyrroles

Special Issue Information

Dear Colleagues,

"... the excited electronic state is to be treated as a new species with its own structure, electron distribution and reactivity ... Since each molecule only has one ground state, but several excited states, it is obvious that this field of work offers more material in the real sense than all conventional chemistry... ". With this statement in the 1967 Nobel lecture, George Porter [1920–2002] had summarized a stimulating vision based on his work on flash photolysis of short-lived species.

On the occasion of George Porter's 100th birthday, this Special Issue will explore where his vision has led by inviting current work on excited states of organic molecules or molecular assemblies. Fifty years ago, research was largely confined to small molecules in physics laboratories. It has since expanded to large multi-chromophoric systems and interdisciplinary cooperation in various fields including biology, medicine, and material science. The laser, first experimentally realized 60 years ago, rendered accessible the variety of excited electronic states of organic molecules. Due to its great variability in wavelength, temporal behavior, and energy, it is the basic tool that has led, for example, to the development and fruitful application of nonlinear spectroscopy.

It will be memorable and at the same time stimulating to present examples of interdisciplinary cooperation between physics, chemistry, biology, medicine, including mathematics, in the research of molecular excited states.

To this end, we welcome the submission of reviews, personal accounts, original research, and perspectives on topics including, but not limited to the following:

Properties and processes in the manifold of excited states of a molecule, including stepwise and simultaneous multiphoton excitation, dark states and optically forbidden transitions, energy transfer, excitonic interactions in systems like dyes, photosensitizers, photosynthetic pigments (chlorophylls, carotenoids, bilins) and protein complexes, melanins, and artificial systems.

Dr. Dieter Leupold
Prof. Dr. Hugo Scheer
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Published Papers (5 papers)

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18 pages, 3719 KiB  
Article
Towards Understanding Excited-State Properties of Organic Molecules Using Time-Resolved Soft X-ray Absorption Spectroscopy
by Holger Stiel, Julia Braenzel, Adrian Jonas, Richard Gnewkow, Lisa Theresa Glöggler, Denny Sommer, Thomas Krist, Alexei Erko, Johannes Tümmler and Ioanna Mantouvalou
Int. J. Mol. Sci. 2021, 22(24), 13463; https://doi.org/10.3390/ijms222413463 - 15 Dec 2021
Cited by 8 | Viewed by 3251
Abstract
The extension of the pump-probe approach known from UV/VIS spectroscopy to very short wavelengths together with advanced simulation techniques allows a detailed analysis of excited-state dynamics in organic molecules or biomolecular structures on a nanosecond to femtosecond time level. Optical pump soft X-ray [...] Read more.
The extension of the pump-probe approach known from UV/VIS spectroscopy to very short wavelengths together with advanced simulation techniques allows a detailed analysis of excited-state dynamics in organic molecules or biomolecular structures on a nanosecond to femtosecond time level. Optical pump soft X-ray probe spectroscopy is a relatively new approach to detect and characterize optically dark states in organic molecules, exciton dynamics or transient ligand-to-metal charge transfer states. In this paper, we describe two experimental setups for transient soft X-ray absorption spectroscopy based on an LPP emitting picosecond and sub-nanosecond soft X-ray pulses in the photon energy range between 50 and 1500 eV. We apply these setups for near-edge X-ray absorption fine structure (NEXAFS) investigations of thin films of a metal-free porphyrin, an aggregate forming carbocyanine and a nickel oxide molecule. NEXAFS investigations have been carried out at the carbon, nitrogen and oxygen K-edge as well as on the Ni L-edge. From time-resolved NEXAFS carbon, K-edge measurements of the metal-free porphyrin first insights into a long-lived trap state are gained. Our findings are discussed and compared with density functional theory calculations. Full article
(This article belongs to the Special Issue Excited Electronic States of Organic Molecules–50 Years of an Interdisciplinary Research —A Tribute to Sir George Porter on the Occasion of His 100th Birthday)
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15 pages, 3079 KiB  
Article
Ultrafast Photoconversion Dynamics of the Knotless Phytochrome SynCph2
by Tobias Fischer, Luuk J. G. W. van Wilderen, Petra Gnau, Jens Bredenbeck, Lars-Oliver Essen, Josef Wachtveitl and Chavdar Slavov
Int. J. Mol. Sci. 2021, 22(19), 10690; https://doi.org/10.3390/ijms221910690 - 2 Oct 2021
Cited by 7 | Viewed by 2708
Abstract
The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the [...] Read more.
The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast Pr ⇆ Pfr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of Pr* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow Pr* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The Pfr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes. Full article
(This article belongs to the Special Issue Excited Electronic States of Organic Molecules–50 Years of an Interdisciplinary Research —A Tribute to Sir George Porter on the Occasion of His 100th Birthday)
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16 pages, 3738 KiB  
Article
The Relationship between the Spatial Arrangement of Pigments and Exciton Transition Moments in Photosynthetic Light-Harvesting Complexes
by Roman Y. Pishchalnikov, Denis D. Chesalin and Andrei P. Razjivin
Int. J. Mol. Sci. 2021, 22(18), 10031; https://doi.org/10.3390/ijms221810031 - 17 Sep 2021
Cited by 2 | Viewed by 2646
Abstract
Considering bacteriochlorophyll molecules embedded in the protein matrix of the light-harvesting complexes of purple bacteria (known as LH2 and LH1-RC) as examples of systems of interacting pigment molecules, we investigated the relationship between the spatial arrangement of the pigments and their exciton transition [...] Read more.
Considering bacteriochlorophyll molecules embedded in the protein matrix of the light-harvesting complexes of purple bacteria (known as LH2 and LH1-RC) as examples of systems of interacting pigment molecules, we investigated the relationship between the spatial arrangement of the pigments and their exciton transition moments. Based on the recently reported crystal structures of LH2 and LH1-RC and the outcomes of previous theoretical studies, as well as adopting the Frenkel exciton Hamiltonian for two-level molecules, we performed visualizations of the LH2 and LH1 exciton transition moments. To make the electron transition moments in the exciton representation invariant with respect to the position of the system in space, a system of pigments must be translated to the center of mass before starting the calculations. As a result, the visualization of the transition moments for LH2 provided the following pattern: two strong transitions were outside of LH2 and the other two were perpendicular and at the center of LH2. The antenna of LH1-RC was characterized as having the same location of the strongest moments in the center of the complex, exactly as in the B850 ring, which actually coincides with the RC. Considering LH2 and LH1 as supermolecules, each of which has excitation energies and corresponding transition moments, we propose that the outer transitions of LH2 can be important for inter-complex energy exchange, while the inner transitions keep the energy in the complex; moreover, in the case of LH1, the inner transitions increased the rate of antenna-to-RC energy transfer. Full article
(This article belongs to the Special Issue Excited Electronic States of Organic Molecules–50 Years of an Interdisciplinary Research —A Tribute to Sir George Porter on the Occasion of His 100th Birthday)
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12 pages, 2179 KiB  
Article
Live Cell Imaging of Enzymatic Turnover of an Adenosine 5′-Tetraphosphate Analog
by Anayat Bhat, Shuang Li, Daniel Hammler, Martin J. Winterhalder, Andreas Marx and Andreas Zumbusch
Int. J. Mol. Sci. 2021, 22(16), 8616; https://doi.org/10.3390/ijms22168616 - 10 Aug 2021
Cited by 1 | Viewed by 2589
Abstract
The hydrolysis of nucleotides is of paramount importance as an energy source for cellular processes. In addition, the transfer of phosphates from nucleotides onto proteins is important as a post-translational protein modification. Monitoring the enzymatic turnover of nucleotides therefore offers great potential as [...] Read more.
The hydrolysis of nucleotides is of paramount importance as an energy source for cellular processes. In addition, the transfer of phosphates from nucleotides onto proteins is important as a post-translational protein modification. Monitoring the enzymatic turnover of nucleotides therefore offers great potential as a tool to follow enzymatic activity. While a number of fluorescence sensors are known, so far, there are no methods available for the real-time monitoring of ATP hydrolysis inside live cells. We present the synthesis and application of a novel fluorogenic adenosine 5′-tetraphosphate (Ap4) analog suited for this task. Upon enzymatic hydrolysis, the molecule displays an increase in fluorescence intensity, which provides a readout of its turnover. We demonstrate how this can be used for monitoring cellular processes involving Ap4 hydrolysis. To this end, we visualized the enzymatic activity in live cells using confocal fluorescence microscopy of the Ap4 analog. Our results demonstrate that the Ap4 analog is hydrolyzed in lysosomes. We show that this approach is suited to visualize the lysosome distribution profiles within the live cell and discuss how it can be employed to gather information regarding autophagic flux. Full article
(This article belongs to the Special Issue Excited Electronic States of Organic Molecules–50 Years of an Interdisciplinary Research —A Tribute to Sir George Porter on the Occasion of His 100th Birthday)
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9 pages, 1365 KiB  
Article
Exciton Origin of Color-Tuning in Ca2+-Binding Photosynthetic Bacteria
by Kõu Timpmann, Margus Rätsep, Liina Kangur, Alexandra Lehtmets, Zheng-Yu Wang-Otomo and Arvi Freiberg
Int. J. Mol. Sci. 2021, 22(14), 7338; https://doi.org/10.3390/ijms22147338 - 8 Jul 2021
Cited by 5 | Viewed by 1996
Abstract
Flexible color adaptation to available ecological niches is vital for the photosynthetic organisms to thrive. Hence, most purple bacteria living in the shade of green plants and algae apply bacteriochlorophyll a pigments to harvest near infra-red light around 850–875 nm. Exceptions are some [...] Read more.
Flexible color adaptation to available ecological niches is vital for the photosynthetic organisms to thrive. Hence, most purple bacteria living in the shade of green plants and algae apply bacteriochlorophyll a pigments to harvest near infra-red light around 850–875 nm. Exceptions are some Ca2+-containing species fit to utilize much redder quanta. The physical basis of such anomalous absorbance shift equivalent to ~5.5 kT at ambient temperature remains unsettled so far. Here, by applying several sophisticated spectroscopic techniques, we show that the Ca2+ ions bound to the structure of LH1 core light-harvesting pigment–protein complex significantly increase the couplings between the bacteriochlorophyll pigments. We thus establish the Ca-facilitated enhancement of exciton couplings as the main mechanism of the record spectral red-shift. The changes in specific interactions such as pigment–protein hydrogen bonding, although present, turned out to be secondary in this regard. Apart from solving the two-decade-old conundrum, these results complement the list of physical principles applicable for efficient spectral tuning of photo-sensitive molecular nano-systems, native or synthetic. Full article
(This article belongs to the Special Issue Excited Electronic States of Organic Molecules–50 Years of an Interdisciplinary Research —A Tribute to Sir George Porter on the Occasion of His 100th Birthday)
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