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Rotational and Vibrational Probes of Biomolecular Structure and Dynamics

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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 28274

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Dr. Maria Eugenia Sanz

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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

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Keywords

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

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Published Papers (10 papers)

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Research

11 pages, 1508 KiB

Open AccessArticle

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://doi.org/10.3390/molecules27103278 - 20 May 2022

Cited by 2 | Viewed by 1919

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 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

Open AccessArticle

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://doi.org/10.3390/molecules27103163 - 15 May 2022

Cited by 7 | Viewed by 2243

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 6^δ and inter-residue 7^δ 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 7^δ 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

Open AccessArticle

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://doi.org/10.3390/molecules27092820 - 28 Apr 2022

Cited by 7 | Viewed by 2672

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, 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 r_S 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

Open AccessArticle

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://doi.org/10.3390/molecules27092639 - 20 Apr 2022

Cited by 4 | Viewed by 2549

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 23 GHz. Two conformers were assigned, one with C_s 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

Open AccessArticle

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://doi.org/10.3390/molecules27072367 - 6 Apr 2022

Cited by 3 | Viewed by 2710

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 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

Open AccessArticle

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://doi.org/10.3390/molecules27072272 - 31 Mar 2022

Cited by 4 | Viewed by 2690

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, 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

Open AccessArticle

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://doi.org/10.3390/molecules27061924 - 16 Mar 2022

Cited by 5 | Viewed by 3220

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 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

Open AccessArticle

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://doi.org/10.3390/molecules27010101 - 24 Dec 2021

Cited by 1 | Viewed by 3312

Abstract

Rotational microwave jet spectroscopy studies of the monoterpenol

α

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

^{- 1} h c

for the protiated and deuterated alcohol, respectively, which further shrink to 9(1) and 3(1) cm

^{- 1} h c

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

Open AccessArticle

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://doi.org/10.3390/molecules27010038 - 22 Dec 2021

Cited by 13 | Viewed by 2946

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 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

Open AccessArticle

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://doi.org/10.3390/molecules26247585 - 14 Dec 2021

Cited by 4 | Viewed by 2654

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 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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