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Special Issue "Vibrational Probes of Biomolecular Structure and Dynamics"

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

Deadline for manuscript submissions: 31 December 2018

Special Issue Editor

Guest Editor
Prof. Dr. Chong Fang

Department of Chemistry, 153 Gilbert Hall, Oregon State University, Corvallis, OR 97331, USA
Website | E-Mail
Phone: 5417376704
Interests: femtosecond Raman; vibrational probes; structural dynamics; fluorescent proteins; photoacids; photophysics and photochemistry; excited state processes; energy relaxation; proton transfer; hydrogen bonding interactions; nonlinear optics; ultrafast spectroscopy

Special Issue Information

Dear Colleagues,

The past few decades have seen tremendous progress in understanding the structure–function relationships of biomolecular systems from microscopic motions to macroscopic properties. Among all the molecular characterization methods, vibrational probes stand out as a versatile and fruitful endeavor because they are highly sensitive to local environment and can be designed, modified, positioned, and controlled to reveal previously unavailable, unknown, or unattainable information about the system under investigation.

The vibrational probes used for steady-state biomolecular structural determination include functional groups and chemical compounds such as carbonyl, nitrile, azide, and cyanamide, while the time-resolved studies can use those characteristic probes to track equilibrium processes (e.g., anharmonic coupling, H-bonding interactions, spectral diffusion, chemical exchange, energy transport) and non-equilibrium processes (e.g., protein folding and unfolding, cooling, electron and proton transfer, transient absorption, fluorescence). Such a wealth of information has been obtained by active researchers across the modern disciplines of physical chemistry and chemical physics, biophysics and biochemistry, ultrafast spectroscopy and nonlinear optics, chemical biology, imaging and microscopy. Individual or pairs of isotopically labeled, engineered or non-natural probes, in conjunction with various advanced spectroscopic and microscopic techniques based on light-matter interactions, have further expanded the repertoire of vibrational toolset.

The aim of this Special Issue is to bring together leading experts across disciplines and highlight recent advances utilizing vibrational probes to study biomolecular structure and dynamics. Both original research articles and reviews are welcome, and articles that report or propose new ideas and new directions to stimulate future development and applications are particularly welcome.

Prof. Dr. Chong Fang
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 papers will be 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 monthly 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 1800 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.


  • structure-function relationships
  • molecular spectroscopy
  • imaging and microscopy
  • protein engineering
  • bioprobe development
  • potential energy surface
  • vibrational dynamics
  • functional motions and interactions
  • equilibrium and non-equilibrium processes

Published Papers (1 paper)

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Open AccessFeature PaperArticle Excited State Structural Evolution of a GFP Single-Site Mutant Tracked by Tunable Femtosecond-Stimulated Raman Spectroscopy
Molecules 2018, 23(9), 2226; https://doi.org/10.3390/molecules23092226
Received: 26 July 2018 / Revised: 29 August 2018 / Accepted: 31 August 2018 / Published: 1 September 2018
PDF Full-text (4139 KB) | HTML Full-text | XML Full-text | Supplementary Files
Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited
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Tracking vibrational motions during a photochemical or photophysical process has gained momentum, due to its sensitivity to the progression of reaction and change of environment. In this work, we implemented an advanced ultrafast vibrational technique, femtosecond-stimulated Raman spectroscopy (FSRS), to monitor the excited state structural evolution of an engineered green fluorescent protein (GFP) single-site mutant S205V. This mutation alters the original excited state proton transfer (ESPT) chain. By strategically tuning the Raman pump to different wavelengths (i.e., 801, 539, and 504 nm) to achieve pre-resonance with transient excited state electronic bands, the characteristic Raman modes of the excited protonated (A*) chromophore species and intermediate deprotonated (I*) species can be selectively monitored. The inhomogeneous distribution/population of A* species go through ESPT with a similar ~300 ps time constant, confirming that bridging a water molecule to protein residue T203 in the ESPT chain is the rate-limiting step. Some A* species undergo vibrational cooling through high-frequency motions on the ~190 ps time scale. At early times, a portion of the largely protonated A* species could also undergo vibrational cooling or return to the ground state with a ~80 ps time constant. On the photoproduct side, a ~1330 cm−1 delocalized motion is observed, with dispersive line shapes in both the Stokes and anti-Stokes FSRS with a pre-resonance Raman pump, which indicates strong vibronic coupling, as the mode could facilitate the I* species to reach a relatively stable state (e.g., the main fluorescent state) after conversion from A*. Our findings disentangle the contributions of various vibrational motions active during the ESPT reaction, and offer new structural dynamics insights into the fluorescence mechanisms of engineered GFPs and other analogous autofluorescent proteins. Full article
(This article belongs to the Special Issue Vibrational Probes of Biomolecular Structure and Dynamics)

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