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Dynamics of Chemical and Biological Systems
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Dynamics of Chemical and Biological Systems

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (15 April 2023) | Viewed by 4772

Special Issue Editor

Prof. Dr. Pratik Sen

E-Mail Website
Guest Editor
Department of Chemistry, IIT Kanpur, Kanpur 208 016, UP, India
Interests: ultrafast excited-state dynamics; electron/proton/energy transfer; associated water dynamics; single molecular biophysics; protein structure dynamics/activity; deep eutectic systems; perovskite nanocrystal; methodologies in fluorescence

Special Issue Information

Dear Colleagues,

Understanding the complexity of chemical and biological systems in terms of chemical and physical principles remains a great challenge in natural science. Recent developments suggest that dynamics at various lengths and timescales control chemistry, and the contemporary focus is to gain physical insight into this control in small molecules, complex biosystems, nanomaterials and solutions. For example, the study of photo physics in a timescale faster/comparable to internal conversion, vibrational cooling and solvent relaxation might provide unique insights to open up new possibilities for reaction dynamics.

In the past, various photophysical processes, e.g., photoinduced large amplitude motion, electron/proton transfer, energy transfer, excimer formation, intersystem crossing, etc., have been studied in various chemical and biochemical systems to understand the role of dynamics in novel molecular phenomena. Conformational protein dynamics have been identified as a key factor that control its activity. Most of the biology occurs in aqueous solution, and associated water dynamics might be a key factor that controls it.

This Special Issue aims to gather scientific manuscripts in areas related to the dynamics of chemical and biological systems. Studies of dynamics at the various lengths and timescales of chemical and biological systems or any other relevant area are welcome to be submitted. 

Prof. Dr. Pratik Sen
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • photophysics
  • ultrafast excited-state dynamics
  • electron transfer
  • proton transfer
  • energy transfer
  • single-molecule biophysics
  • associated water dynamics
  • protein structure dynamics/activity
  • heterogeneity

Published Papers (3 papers)

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Research

15 pages, 1846 KiB  
Article
Conformational Changes in Surface-Immobilized Proteins Measured Using Combined Atomic Force and Fluorescence Microscopy
by Cristian Staii
Molecules 2023, 28(12), 4632; https://doi.org/10.3390/molecules28124632 - 8 Jun 2023
Cited by 2 | Viewed by 1023
Abstract
Biological organisms rely on proteins to perform the majority of their functions. Most protein functions are based on their physical motions (conformational changes), which can be described as transitions between different conformational states in a multidimensional free-energy landscape. A comprehensive understanding of this [...] Read more.
Biological organisms rely on proteins to perform the majority of their functions. Most protein functions are based on their physical motions (conformational changes), which can be described as transitions between different conformational states in a multidimensional free-energy landscape. A comprehensive understanding of this free-energy landscape is therefore of paramount importance for understanding the biological functions of proteins. Protein dynamics includes both equilibrium and nonequilibrium motions, which typically exhibit a wide range of characteristic length and time scales. The relative probabilities of various conformational states in the energy landscape, the energy barriers between them, their dependence on external parameters such as force and temperature, and their connection to the protein function remain largely unknown for most proteins. In this paper, we present a multimolecule approach in which the proteins are immobilized at well-defined locations on Au substrates using an atomic force microscope (AFM)-based patterning method called nanografting. This method enables precise control over the protein location and orientation on the substrate, as well as the creation of biologically active protein ensembles that self-assemble into well-defined nanoscale regions (protein patches) on the gold substrate. We performed AFM–force compression and fluorescence experiments on these protein patches and measured the fundamental dynamical parameters such as protein stiffness, elastic modulus, and transition energies between distinct conformational states. Our results provide new insights into the processes that govern protein dynamics and its connection to protein function. Full article
(This article belongs to the Special Issue Dynamics of Chemical and Biological Systems)
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29 pages, 7072 KiB  
Article
Photogrammetry of Ultrafast Excited-State Intramolecular Proton Transfer Pathways in the Fungal Pigment Draconin Red
by Janak Solaris, Taylor D. Krueger, Cheng Chen and Chong Fang
Molecules 2023, 28(8), 3506; https://doi.org/10.3390/molecules28083506 - 16 Apr 2023
Cited by 1 | Viewed by 1802
Abstract
Proton transfer processes of organic molecules are key to charge transport and photoprotection in biological systems. Among them, excited-state intramolecular proton transfer (ESIPT) reactions are characterized by quick and efficient charge transfer within a molecule, resulting in ultrafast proton motions. The ESIPT-facilitated interconversion [...] Read more.
Proton transfer processes of organic molecules are key to charge transport and photoprotection in biological systems. Among them, excited-state intramolecular proton transfer (ESIPT) reactions are characterized by quick and efficient charge transfer within a molecule, resulting in ultrafast proton motions. The ESIPT-facilitated interconversion between two tautomers (PS and PA) comprising the tree fungal pigment Draconin Red in solution was investigated using a combination of targeted femtosecond transient absorption (fs-TA) and excited-state femtosecond stimulated Raman spectroscopy (ES-FSRS) measurements. Transient intensity (population and polarizability) and frequency (structural and cooling) dynamics of –COH rocking and –C=C, –C=O stretching modes following directed stimulation of each tautomer elucidate the excitation-dependent relaxation pathways, particularly the bidirectional ESIPT progression out of the Franck–Condon region to the lower-lying excited state, of the intrinsically heterogeneous chromophore in dichloromethane solvent. A characteristic overall excited-state PS-to-PA transition on the picosecond timescale leads to a unique “W”-shaped excited-state Raman intensity pattern due to dynamic resonance enhancement with the Raman pump–probe pulse pair. The ability to utilize quantum mechanics calculations in conjunction with steady-state electronic absorption and emission spectra to induce disparate excited-state populations in an inhomogeneous mixture of similar tautomers has broad implications for the modeling of potential energy surfaces and delineation of reaction mechanisms in naturally occurring chromophores. Such fundamental insights afforded by in-depth analysis of ultrafast spectroscopic datasets are also beneficial for future development of sustainable materials and optoelectronics. Full article
(This article belongs to the Special Issue Dynamics of Chemical and Biological Systems)
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10 pages, 2570 KiB  
Article
Dynamics of Electron Transfers in Photosensitization Reactions of Zinc Porphyrin Derivatives
by Soohwan Kim, Taesoo Kim, Sunghan Choi, Ho-Jin Son, Sang Ook Kang and Jae Yoon Shin
Molecules 2023, 28(1), 327; https://doi.org/10.3390/molecules28010327 - 31 Dec 2022
Viewed by 1558
Abstract
Photocatalytic systems for CO2 reduction operate via complicated multi-electron transfer (ET) processes. A complete understanding of these ET dynamics can be challenging but is key to improving the efficiency of CO2 conversion. Here, we report the ET dynamics of a series [...] Read more.
Photocatalytic systems for CO2 reduction operate via complicated multi-electron transfer (ET) processes. A complete understanding of these ET dynamics can be challenging but is key to improving the efficiency of CO2 conversion. Here, we report the ET dynamics of a series of zinc porphyrin derivatives (ZnPs) in the photosensitization reactions where sequential ET reactions of ZnPs occur with a sacrificial electron donor (SED) and then with TiO2. We employed picosecond time-resolved fluorescence spectroscopy and femtosecond transient absorption (TA) measurement to investigate the fast ET dynamics concealed in the steady-state or slow time-resolved measurements. As a result, Stern-Volmer analysis of fluorescence lifetimes evidenced that the reaction of photoexcited ZnPs with SED involves static and dynamic quenching. The global fits to the TA spectra identified much faster ET dynamics on a few nanosecond-time scales in the reactions of one-electron reduced species (ZnPs•–) with TiO2 compared to previously measured minute-scale quenching dynamics and even diffusion rates. We propose that these dynamics report the ET dynamics of ZnPs•– formed at adjacent TiO2 without involving diffusion. This study highlights the importance of ultrafast time-resolved spectroscopy for elucidating the detailed ET dynamics in photosensitization reactions. Full article
(This article belongs to the Special Issue Dynamics of Chemical and Biological Systems)
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