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Rotational and Vibrational Probes of Biomolecular Structure and Dynamics
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Rotational and 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: closed (31 March 2022) | Viewed by 23230

Special Issue Editor

Dr. Maria Eugenia Sanz

E-Mail Website
Guest Editor
Department of Chemistry, King's College London, London SE11DB, UK
Interests: non-covalent interactions; hydrogen bonding; structural and conformational determination; rotational spectroscopy; computational chemistry; molecular clusters

Special Issue Information

Dear Colleagues,

The structure and dynamics of biomolecules determine their function, response to light, and interactions with other molecules. Characterising the specific features that influence biomolecular behaviour is vital to advance our understanding of nature and develop biomimetic species with enhanced properties, tuned to respond to technological and societal challenges. Spectroscopic techniques are key in advancing our knowledge of biomolecules. Their use by researchers across physics, chemistry, and chemical biology have yielded fundamental insights into a large variety of biomolecular systems. In particular, rotational and vibrational spectroscopic probes in frequency-resolved and time-resolved experiments have revealed previously unattainable information, due to their high resolution and sensitivity.

To highlight and celebrate current developments in this field, our journal Molecules will launch a Special Issue on “Rotational and Vibrational Probes of Biomolecular Structure and Dynamics”, to be published in 2021. We encourage the contribution of high-quality papers and review articles in all areas of physical chemistry involved in the interrogation of biomolecular systems by spectroscopic rotational and vibrational tools, at the molecular level. We hope that submissions will show the diversity and potential of this field.  

We look forward to receiving your contributions.

Dr. Maria Sanz
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

  • Biomolecules
  • Molecular spectroscopy
  • Structural determination
  • Ultrafast chemistry
  • Biomolecular interactions
  • Experimental and theoretical studies

Published Papers (10 papers)

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Research

11 pages, 1508 KiB  
Article
Spectroscopic Characterization of 3-Aminoisoxazole, a Prebiotic Precursor of Ribonucleotides
by Alessio Melli, Mattia Melosso, Kevin G. Lengsfeld, Luca Bizzocchi, Víctor M. Rivilla, Luca Dore, Vincenzo Barone, Jens-Uwe Grabow and Cristina Puzzarini
Molecules 2022, 27(10), 3278; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27103278 - 20 May 2022
Cited by 2 | Viewed by 1565
Abstract
The processes and reactions that led to the formation of the first biomolecules on Earth play a key role in the highly debated theme of the origin of life. Whether the first chemical building blocks were generated on Earth (endogenous synthesis) or brought [...] Read more.
The processes and reactions that led to the formation of the first biomolecules on Earth play a key role in the highly debated theme of the origin of life. Whether the first chemical building blocks were generated on Earth (endogenous synthesis) or brought from space (exogenous delivery) is still unanswered. The detection of complex organic molecules in the interstellar medium provides valuable support to the latter hypothesis. To gather more insight, here we provide the astronomers with accurate rotational frequencies to guide the interstellar search of 3-aminoisoxazole, which has been recently envisaged as a key reactive species in the scenario of the so-called RNA-world hypothesis. Relying on an accurate computational characterization, we were able to register and analyze the rotational spectrum of 3-aminoisoxazole in the 6–24 GHz and 80–320 GHz frequency ranges for the first time, exploiting a Fourier-transform microwave spectrometer and a frequency-modulated millimeter/sub-millimeter spectrometer, respectively. Due to the inversion motion of the −NH2 group, two states arise, and both of them were characterized, with more than 1300 lines being assigned. Although the fit statistics were affected by an evident Coriolis interaction, we were able to produce accurate line catalogs for astronomical observations of 3-aminoisoxazole. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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15 pages, 3153 KiB  
Article
Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry
by Gildas Goldsztejn, Venkateswara Rao Mundlapati, Valérie Brenner, Eric Gloaguen and Michel Mons
Molecules 2022, 27(10), 3163; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27103163 - 15 May 2022
Cited by 5 | Viewed by 1739
Abstract
The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6δ and inter-residue 7δ H-bonds. The aim of the present article is to document how the substitution [...] Read more.
The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6δ and inter-residue 7δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm−1 spectral shift of the NH stretch engaged in a 7δ NH⋯S/Se bond. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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14 pages, 5220 KiB  
Article
The Shapes of Sulfonamides: A Rotational Spectroscopy Study
by Annalisa Vigorito, Camilla Calabrese, Assimo Maris, Donatella Loru, Isabel Peña, M. Eugenia Sanz and Sonia Melandri
Molecules 2022, 27(9), 2820; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27092820 - 28 Apr 2022
Cited by 7 | Viewed by 2120
Abstract
Benzenesulfonamides are a class of molecules of extreme interest in the biochemical field because many of them are active against a variety of diseases. In this work, the pharmacophoric group benzensulfonamide, its derivatives para-toluensulfonamide and ortho-toluensulfonamide, and the bioactive molecule sulfanilamide, [...] Read more.
Benzenesulfonamides are a class of molecules of extreme interest in the biochemical field because many of them are active against a variety of diseases. In this work, the pharmacophoric group benzensulfonamide, its derivatives para-toluensulfonamide and ortho-toluensulfonamide, and the bioactive molecule sulfanilamide, were investigated using rotational spectroscopy to determine their conformations and the influence of different substituents on their structures. For all species, the hyperfine structure due to the 14N atom was analyzed, and this provided crucial information for the unambiguous identification of the observed conformation of all molecules. In addition, for ortho-toluensulfonamide, the vibration–rotation hyperfine structure related to the methyl torsion was analyzed, and the methyl group rotation barrier was determined. For benzensulfonamide, partial rS and r0 structures were established from the experimental rotational constants of the parent and two deuterated isotopic species. In all compounds except ortho-toluensulfonamide, the amino group of the sulfonamide group lies perpendicular to the benzene plane with the aminic hydrogens eclipsing the oxygen atoms. In ortho-toluensulfonamide, where weak attractive interactions occur between the nitrogen lone pair and the methyl hydrogen atoms, the amino group lies in a gauche orientation, retaining the eclipsed configuration with respect to the SO2 frame. A comparison of the geometrical arrangements found in the PDB database allowed us to understand that the bioactive conformations are different from those found in isolated conditions. The conformations within the receptor are reached with an energy cost, which is balanced by the interactions established in the receptor. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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12 pages, 2455 KiB  
Article
Methyl Internal Rotation in Fruit Esters: Chain-Length Effect Observed in the Microwave Spectrum of Methyl Hexanoate
by Nhu-Ngoc Dang, Hoang-Nam Pham, Isabelle Kleiner, Martin Schwell, Jens-Uwe Grabow and Ha Vinh Lam Nguyen
Molecules 2022, 27(9), 2639; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27092639 - 20 Apr 2022
Cited by 3 | Viewed by 2045
Abstract
The gas-phase structures of the fruit ester methyl hexanoate, CH3-O-(C=O)-C5H11, have been determined using a combination of molecular jet Fourier-transform microwave spectroscopy and quantum chemistry. The microwave spectrum was measured in the frequency range of 3 to [...] Read more.
The gas-phase structures of the fruit ester methyl hexanoate, CH3-O-(C=O)-C5H11, have been determined using a combination of molecular jet Fourier-transform microwave spectroscopy and quantum chemistry. The microwave spectrum was measured in the frequency range of 3 to 23 GHz. Two conformers were assigned, one with Cs symmetry and the other with C1 symmetry where the γ-carbon atom of the hexyl chain is in a gauche orientation in relation to the carbonyl bond. Splittings of all rotational lines into doublets were observed due to internal rotation of the methoxy methyl group CH3-O, from which torsional barriers of 417 cm−1 and 415 cm−1, respectively, could be deduced. Rotational constants obtained from geometry optimizations at various levels of theory were compared to the experimental values, confirming the soft degree of freedom of the (C=O)-C bond observed for the C1 conformer of shorter methyl alkynoates like methyl butyrate and methyl valerate. Comparison of the barriers to methyl internal rotation of methyl hexanoate to those of other CH3-O-(C=O)-R molecules leads to the conclusion that though the barrier height is relatively constant at about 420 cm−1, it decreases in molecules with longer R. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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18 pages, 1723 KiB  
Article
Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy
by Iuliia Stroganova, Sjors Bakels and Anouk M. Rijs
Molecules 2022, 27(7), 2367; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27072367 - 06 Apr 2022
Cited by 2 | Viewed by 2138
Abstract
Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of [...] Read more.
Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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14 pages, 2514 KiB  
Article
Investigating the Ultrafast Dynamics and Long-Term Photostability of an Isomer Pair, Usujirene and Palythene, from the Mycosporine-like Amino Acid Family
by Abigail L. Whittock, Jack M. Woolley, Nazia Auckloo, Christophe Corre and Vasilios G. Stavros
Molecules 2022, 27(7), 2272; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27072272 - 31 Mar 2022
Cited by 4 | Viewed by 2208
Abstract
Mycosporine-like amino acids are a prevalent form of photoprotection in micro- and macro-organisms. Using a combination of natural product extraction/purification and femtosecond transient absorption spectroscopy, we studied the relaxation pathway for a common mycosporine-like amino acid pair, usujirene and its geometric isomer palythene, [...] Read more.
Mycosporine-like amino acids are a prevalent form of photoprotection in micro- and macro-organisms. Using a combination of natural product extraction/purification and femtosecond transient absorption spectroscopy, we studied the relaxation pathway for a common mycosporine-like amino acid pair, usujirene and its geometric isomer palythene, in the first few nanoseconds following photoexcitation. Our studies show that the electronic excited state lifetimes of these molecules persist for only a few hundred femtoseconds before the excited state population is funneled through an energetically accessible conical intersection with subsequent vibrational energy transfer to the solvent. We found that a minor portion of the isomer pair did not recover to their original state within 3 ns after photoexcitation. We investigated the long-term photostability using continuous irradiation at a single wavelength and with a solar simulator to mimic a more real-life environment; high levels of photostability were observed in both experiments. Finally, we employed computational methods to elucidate the photochemical and photophysical properties of usujirene and palythene as well as to reconcile the photoprotective mechanism. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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11 pages, 2104 KiB  
Article
Rotational Spectrum and Conformational Analysis of Perillartine: Insights into the Structure–Sweetness Relationship
by Gabriela Juárez, Miguel Sanz-Novo, José L. Alonso, Elena R. Alonso and Iker León
Molecules 2022, 27(6), 1924; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27061924 - 16 Mar 2022
Cited by 1 | Viewed by 2646
Abstract
We used high-resolution rotational spectroscopy coupled to a laser ablation source to study the conformational panorama of perillartine, a solid synthetic sweetener. Four conformers were identified under the isolation conditions of the supersonic expansion, showing that all of them present an E configuration [...] Read more.
We used high-resolution rotational spectroscopy coupled to a laser ablation source to study the conformational panorama of perillartine, a solid synthetic sweetener. Four conformers were identified under the isolation conditions of the supersonic expansion, showing that all of them present an E configuration of the C=N group with respect to the double bond of the ring. The observed structures were verified against Shallenberger–Acree–Kier’s sweetness theory to shed light on the structure–sweetness relationship for this particular oxime, highlighting a deluge of possibilities to bind the receptor. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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29 pages, 7640 KiB  
Article
Hydrogen Delocalization in an Asymmetric Biomolecule: The Curious Case of Alpha-Fenchol
by Robert Medel, Johann R. Springborn, Deborah L. Crittenden and Martin A. Suhm
Molecules 2022, 27(1), 101; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27010101 - 24 Dec 2021
Cited by 1 | Viewed by 2840
Abstract
Rotational microwave jet spectroscopy studies of the monoterpenol α-fenchol have so far failed to identify its second most stable torsional conformer, despite computational predictions that it is only very slightly higher in energy than the global minimum. Vibrational FTIR and Raman jet [...] Read more.
Rotational microwave jet spectroscopy studies of the monoterpenol α-fenchol have so far failed to identify its second most stable torsional conformer, despite computational predictions that it is only very slightly higher in energy than the global minimum. Vibrational FTIR and Raman jet spectroscopy investigations reveal unusually complex OH and OD stretching spectra compared to other alcohols. Via modeling of the torsional states, observed spectral splittings are explained by delocalization of the hydroxy hydrogen atom through quantum tunneling between the two non-equivalent but accidentally near-degenerate conformers separated by a low and narrow barrier. The energy differences between the torsional states are determined to be only 16(1) and 7(1) cm−1hc for the protiated and deuterated alcohol, respectively, which further shrink to 9(1) and 3(1) cm−1hc upon OH or OD stretch excitation. Comparisons are made with the more strongly asymmetric monoterpenols borneol and isopinocampheol as well as with the symmetric, rapidly tunneling propargyl alcohol. In addition, the third—in contrast localized—torsional conformer and the most stable dimer are assigned for α-fenchol, as well as the two most stable dimers for propargyl alcohol. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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19 pages, 4308 KiB  
Article
Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes
by Haolu Wang, Matthias Heger, Mohamad H. Al-Jabiri and Yunjie Xu
Molecules 2022, 27(1), 38; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27010038 - 22 Dec 2021
Cited by 9 | Viewed by 2518
Abstract
The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary [...] Read more.
The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol−1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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14 pages, 24585 KiB  
Article
Decoding the Structure of Non-Proteinogenic Amino Acids: The Rotational Spectrum of Jet-Cooled Laser-Ablated Thioproline
by Juan Carlos López, Alberto Macario, Andrés Verde, Alfonso Pérez-Encabo and Susana Blanco
Molecules 2021, 26(24), 7585; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26247585 - 14 Dec 2021
Cited by 4 | Viewed by 2171
Abstract
The broadband rotational spectrum of jet-cooled laser-ablated thioproline was recorded. Two conformers of this system were observed and identified with the help of DFT and ab initio computations by comparison of the observed and calculated rotational constants and 14N quadrupole coupling constants [...] Read more.
The broadband rotational spectrum of jet-cooled laser-ablated thioproline was recorded. Two conformers of this system were observed and identified with the help of DFT and ab initio computations by comparison of the observed and calculated rotational constants and 14N quadrupole coupling constants as well as the predicted energies compared to the observed relative populations. These conformers showed a mixed bent/twisted arrangement of the five-membered ring similar to that of the related compound thiazolidine with the N–H bond in axial configuration. The most stable form had the COOH group in an equatorial position on the same side of the ring as N-H. The arrangement of the C=O group close to the N-H bond led to a weak interaction between them (classified as type I) characterized by a noncovalent interaction analysis. The second form had a trans-COOH arrangement showing a type II O–H···N hydrogen bond. In thioproline, the stability of conformers of type I and type II was reversed with respect to proline. We show how the conformation of the ring depends on the function associated with the endocyclic N atom when comparing the structures of isolated thioproline with its zwitterion observed in condensed phases and with peptide forms. Full article
(This article belongs to the Special Issue Rotational and Vibrational Probes of Biomolecular Structure and Dynamics)
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