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Structural Characterization of Biomolecules by Spectroscopic Methods

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

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 7357

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Special Issue Editors

Prof. Dr. José L. Alonso

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Guest Editor

Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
Interests: high-resolution molecular spectroscopy; rotational spectroscopy; structure of biomolecules; interstellar molecules; inter- and intramolecular interactions; laser ablation techniques

Dr. Elena R. Alonso Alonso

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Guest Editor

Grupo de Espectroscopia Molecular (GEM), Department of Physical Chemistry and Inorganic Chemistry, Universidad de Valladolid, Valladolid, Spain
Interests: rotational spectroscopy; biomolecules; interstellar molecules; laser ablation techniques; millimeter-wave spectroscopy

Dr. Iker León

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Guest Editor

Special Issue Information

Dear Colleagues,

This Special Issue of Molecules is dedicated to the structural characterization of biomolecules through molecular spectroscopic techniques. The structures of biomolecules result from a subtle yet complex balance between many different intrinsic and environmental interactions. Therefore, a molecular level of characterization, interpretation, and knowledge of the different geometries adopted by biomolecules will advance our understanding of the chemical and physical processes involved, which is crucial to gaining insight into their biological functions. Molecular spectroscopic techniques have emerged as promising tools for unearthing the mystery of the structure–property relationship and are at the heart of modern molecular approaches to understanding complex biomolecular systems.

This Special Issue aims to provide a common platform for researchers to share their investigations and findings in the field of Molecular Spectroscopy. It will fulfill the lack of precise structural information on biomolecules and their structure–functionality connection by providing the latest challenges and developments in this promising field.

Prof. Dr. José L. Alonso
Dr. Elena R. Alonso Alonso
Dr. Iker León
Guest Editors

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

molecular spectroscopy
biomolecules
structural characterization
computational studies
experimental-theoretical synergy
structure-property relationship

Published Papers (4 papers)

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Research

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14 pages, 593 KiB

Open AccessArticle

Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks

by Vincenzo Barone, Silvia Di Grande and Cristina Puzzarini

Molecules 2023, 28(2), 913; https://doi.org/10.3390/molecules28020913 - 16 Jan 2023

Cited by 12 | Viewed by 2242

Abstract

The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules. Full article

(This article belongs to the Special Issue Structural Characterization of Biomolecules by Spectroscopic Methods)

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13 pages, 1931 KiB

Open AccessArticle

The Conformations of Isolated Gallic Acid: A Laser-Ablation Rotational Study

by Andrés Verde, Susana Blanco and Juan Carlos López

Molecules 2023, 28(1), 159; https://doi.org/10.3390/molecules28010159 - 24 Dec 2022

Viewed by 1388

Abstract

The rotational spectrum of laser-ablated gallic acid has been recorded using CP-FTMW spectroscopy. Two rotamers have been detected, and their rotational spectra have been assigned and analyzed to obtain the molecular spectroscopic parameters. The observed rotamers have been unambiguously identified in the light of theoretical computations, based on the comparison of the experimental line intensities and rotational parameters with the rotational constants and electric dipole moments predicted from theoretical calculations. The values of the planar inertial moments confirm that the observed conformers are planar, and their relative stability and population have been determined from relative intensity measurements. The B3LYP-D3/6-311++G(2d,p) level has been shown to be the best method among a series of levels normally used to predict the rotational parameters in rotational spectroscopy. In the observed conformers, the three adjacent OH groups are arranged in a sequential form, and the only difference between them lies in the orientation of the COOH group. Although weak attractive OH···O interactions seem to exist, the analysis of the electron density topology does not show the existence of any critical point corresponding to these interactions. Full article

(This article belongs to the Special Issue Structural Characterization of Biomolecules by Spectroscopic Methods)

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14 pages, 1041 KiB

Open AccessArticle

How Water Interacts with the NOH Group: The Rotational Spectrum of the 1:1 N,N-diethylhydroxylamine·Water Complex

by Giovanna Salvitti, Filippo Baroncelli, Chiara Nicotri, Luca Evangelisti, Sonia Melandri and Assimo Maris

Molecules 2022, 27(23), 8190; https://doi.org/10.3390/molecules27238190 - 24 Nov 2022

Cited by 5 | Viewed by 1509

Abstract

The rotational spectrum of the 1:1 N,N-diethylhydroxylamine-water complex has been investigated using pulsed jet Fourier transform microwave spectroscopy in the 6.5–18.5 GHz frequency region. The most stable conformer has been detected as well as the

^{13}

C monosubstituted isotopologues in natural abundance and [...] Read more.

^{13}

C monosubstituted isotopologues in natural abundance and the

^{18}

O enriched water species, allowing to determine the nitrogen nuclear quadrupole coupling constants and the molecular structure in the vibrational ground state. The molecule has a

C_{s}

symmetry and the water lies in the

b c

symmetry plane forming two hydrogen bonds with the NOH frame with length:

d_{HOH \cdot NOH}

= 1.974 Å and

d_{H_{2} O \cdot HON}

= 2.096 Å. From symmetry-adapted perturbation theory calculations coupled to atoms in molecule approach, the corresponding interaction energy values are estimated to be 24 and 13 kJ·mol

^{- 1}

, respectively. The great strength of the intermolecular interaction involving the nitrogen atom is in agreement with the high reactivity of hydroxylamine compounds at the nitrogen site. Full article

(This article belongs to the Special Issue Structural Characterization of Biomolecules by Spectroscopic Methods)

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Review

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19 pages, 5216 KiB

Open AccessReview

Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers

by Katrin Ha Phuong Vu, Gerhard Heinrich Blankenburg, Leonardo Lesser-Rojas and Chia-Fu Chou

Molecules 2022, 27(19), 6448; https://doi.org/10.3390/molecules27196448 - 30 Sep 2022

Cited by 1 | Viewed by 1616

Abstract

Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies. Full article

(This article belongs to the Special Issue Structural Characterization of Biomolecules by Spectroscopic Methods)

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