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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 23817

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Dr. Magdalena Sałdyka

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Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
Interests: molecular interactions; conformational analysis; photochemistry of molecular systems; matrix isolation technique; theoretical modelling of molecular interactions and spectroscopic properties; infrared spectroscopy as a basic tool in molecular structure determination; spectroscopic analytical analysis
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Maria Wierzejewska

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Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
Interests: photochemistry; molecular interactions; conformational analysis; matrix isolation technique; theoretical modelling of molecular interactions and spectroscopic properties

Special Issue Information

Dear Colleagues,

It is my great pleasure to invite you to submit an article for a Special Issue of Molecules on the theme “Advances in Computational Spectroscopy”.

The increasing sophistication of the experimental spectroscopic techniques makes the results increasingly difficult to interpret without the help of computational chemistry. Computational spectroscopy connecting quantum mechanics, molecular spectroscopy and computational chemistry is constantly developing as a tool to provide predictions of spectroscopic characteristics and properties. Quantum chemistry has reached such an accuracy that it can be used to plan and lead experimental research, participate in determination of the spectroscopic parameters, and to obtain the desired results or information. On the other hand, experimental data are suitable for benchmarking theoretical results or introducing new methods of calculation.

It is our hope that this Issue will highlight the achievements in the field of computational spectroscopy on topics such as single-molecule studies as well as simulations of clusters and the solid state, research on organic molecules and inorganic complexes, basic studies as well as different application areas.

Manuscripts describing original research, perspectives, and reviews focusing on computational spectroscopy will be welcome in this Special Issue.

Dr. Magdalena Sałdyka
Prof. Dr. Maria Wierzejewska
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

spectroscopy
computational spectroscopy in inorganic chemistry
computational spectroscopy in bioinorganic chemistry
computational spectroscopy in biological systems
molecular and supramolecular structure
crystal structure
molecular modeling
molecular simulation
molecular dynamics
periodic methods
density functional theory (DFT)
time-dependent DFT (TD-DFT)

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Published Papers (11 papers)

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Research

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18 pages, 764 KiB

Open AccessArticle

Computational Protocol for the Identification of Candidates for Radioastronomical Detection and Its Application to the C₃H₃NO Family of Isomers

by Silvia Alessandrini, Mattia Melosso, Víctor M. Rivilla, Luca Bizzocchi and Cristina Puzzarini

Molecules 2023, 28(7), 3226; https://doi.org/10.3390/molecules28073226 - 4 Apr 2023

Cited by 6 | Viewed by 1754

Abstract

The C₃H₃NO family of isomers is relevant in astrochemistry, even though its members are still elusive in the interstellar medium. To identify the best candidate for astronomical detection within this family, we developed a new computational protocol based on the minimum-energy principle. This approach aims to identify the most stable isomer of the family and consists of three steps. The first step is an extensive investigation that characterizes the vast number of compounds having the C₃H₃NO chemical formula, employing density functional theory for this purpose. The second step is an energy refinement, which is used to select isomers and relies on coupled cluster theory. The last step is a structural improvement with a final energy refinement that provides improved energies and a large set of accurate spectroscopic parameters for all isomers lying within 30 kJ mol⁻¹ above the most stable one. According to this protocol, vinylisocyanate is the most stable isomer, followed by oxazole, which is about 5 kJ mol⁻¹ higher in energy. The other stable species are pyruvonitrile, cyanoacetaldehyde, and cyanovinylalcohol. For all of these species, new computed rotational and vibrational spectroscopic data are reported, which complement those already available in the literature or fill current gaps. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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19 pages, 4705 KiB

Open AccessArticle

Experimental, Spectroscopic, and Computational Insights into the Reactivity of “Methanal” with 2-Naphthylamines

by Martin Havlík, Tereza Navrátilová, Michaela Drozdová, Ameneh Tatar, Priscila A. Lanza, Diego Dusso, Elizabeth Laura Moyano, Carlos A. Chesta, Domingo Mariano A. Vera and Bohumil Dolenský

Molecules 2023, 28(4), 1549; https://doi.org/10.3390/molecules28041549 - 6 Feb 2023

Cited by 1 | Viewed by 1923

Abstract

The reactions of 2-naphthylamine and methyl 6-amino-2-naphthoate with formalin and paraformaldehyde were studied experimentally, spectrally, and by quantum chemical calculations. It was found that neither the corresponding aminals nor imines were formed under the described conditions but could be prepared and spectrally characterized at least in situ under modified conditions. Several of the previously undescribed intermediates and by-products were isolated or at least spectrally characterized. First principle density functional theory (DFT) calculations were performed to shed light on the key aspects of the thermochemistry of decomposition and further condensation of the corresponding aminals and imines. The calculations also revealed that the electrophilicity of methanal was significantly greater than that of ordinary oxo-compounds, except for perfluorinated ones. In summary, methanal was not behaving as the simplest aldehyde but as a very electron-deficient oxo-compound. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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13 pages, 3314 KiB

Open AccessArticle

The Effect of Alkali Iodide Salts in the Inclusion Process of Phenolphthalein in β-Cyclodextrin: A Spectroscopic and Theoretical Study

by Constantine Kouderis, Stefanos Tsigoias, Panagiota Siafarika and Angelos G. Kalampounias

Molecules 2023, 28(3), 1147; https://doi.org/10.3390/molecules28031147 - 23 Jan 2023

Cited by 6 | Viewed by 1869

Abstract

The formation of the inclusion complex between β-cyclodextrin (CD) and phenolphthalein (PP) was investigated by means of UV–Vis and FT-IR spectroscopies. The thermodynamic parameters were calculated in the absence and presence of LiI, KI, NaI and CsI iodide salts. The enthalpy change during the formation was found to be negative for all solutions with iodide salts. The enthalpy change was found to decrease in the sequence no salt > NaI > KI> CsI > LiI. Moreover, it was observed that with increasing salt concentration enthalpy decreases monotonically. The interaction between the two molecules was mostly attributed to hydrogen bonding and Van der Waals interactions. Thermodynamic properties revealed that electrostatic forces also contribute when LiI is present in solutions. A molecular docking study was performed to elucidate the docking between phenolphthalein and cyclodextrin. The FT-IR spectra of CD, PP and the CD–PP complex were recorded to establish the formation of the inclusion complex. Semi-empirical and DFT methods were utilized to study theoretically the complexation process and calculate the IR vibrational spectra. The adequate agreement between theoretical and experimental results supports the proposed structural model for the CD–PP complexation. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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19 pages, 2171 KiB

Open AccessArticle

Infrared Spectra and Phototransformations of meta-Fluorophenol Isolated in Argon and Nitrogen Matrices

by A. J. Lopes Jesus, Juracy Regis de Lucena Júnior, Rui Fausto and Igor Reva

Molecules 2022, 27(23), 8248; https://doi.org/10.3390/molecules27238248 - 26 Nov 2022

Cited by 5 | Viewed by 1893

Abstract

Monomers of meta-fluorophenol (mFP) were trapped from the gas phase into cryogenic argon and nitrogen matrices. The estimated relative energies of the two conformers are very close, and in the gas phase they have nearly equal populations. Due to the similarity of their structures (they only differ in the orientation of the OH group), the two conformers have also similar predicted vibrational signatures, which makes the vibrational characterization of the individual rotamers challenging. In the present work, it has been established that in an argon matrix only the most stable trans conformer of mFP exists (the OH group pointing away from the fluorine atom). On the other hand, the IR spectrum of mFP in a nitrogen matrix testifies to the simultaneous presence in this matrix of both the trans conformer and of the higher-energy cis conformer (the OH group pointing toward the fluorine atom), which is stabilized by interaction with the matrix gas host. We found that the exposition of the cryogenic N₂ matrix to the Globar source of the infrared spectrometer affects the conformational populations. By collecting experimental spectra, either in the full mid-infrared range or only in the range below 2200 cm⁻¹, we were able to reliably distinguish two sets of experimental bands originating from individual conformers. A comparison of the two sets of experimental bands with computed infrared spectra of the conformers allowed, for the first time, the unequivocal vibrational identification of each of them. The joint implementation of computational vibrational spectroscopy and matrix-isolation infrared spectroscopy proved to be a very accurate method of structural analysis. Some mechanistic insights into conformational isomerism (the quantum tunneling of hydrogen atom and vibrationally-induced conformational transformations) have been addressed. Finally, we also subjected matrix-isolated mFP to irradiations with UV light, and the phototransformations observed in these experiments are also described. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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19 pages, 2044 KiB

Open AccessArticle

A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole

by Cheng Giuseppe Chen, Massimiliano Aschi, Marco D’Abramo and Andrea Amadei

Molecules 2022, 27(23), 8135; https://doi.org/10.3390/molecules27238135 - 22 Nov 2022

Cited by 4 | Viewed by 1660

Abstract

In this paper, we introduce specific approximations to simplify the vibronic treatment in modeling absorption and emission spectra, allowing us to include a huge number of vibronic transitions in the calculations. Implementation of such a simplified vibronic treatment within our general approach for modelling vibronic spectra, based on molecular dynamics simulations and the perturbed matrix method, provided a quantitative reproduction of the absorption and emission spectra of aqueous indole with higher accuracy than the one obtained when using the existing vibronic treatment. Such results, showing the reliability of the approximations employed, indicate that the proposed method can be a very efficient and accurate tool for computational spectroscopy. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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18 pages, 4741 KiB

Open AccessArticle

A DFT Study on the Excited Electronic States of Cyanopolyynes: Benchmarks and Applications

by Marcin Gronowski and Robert Kołos

Molecules 2022, 27(18), 5829; https://doi.org/10.3390/molecules27185829 - 8 Sep 2022

Cited by 4 | Viewed by 2016

Abstract

Highly unsaturated chain molecules are interesting due to their potential application as nanowires and occurrence in interstellar space. Here, we focus on predicting the electronic spectra of polyynic nitriles HC_2m+1N (m = 0–13) and dinitriles NC_2n+2N (n = 0–14). The results of time-dependent density functional theory (TD-DFT) calculations are compared with the available gas-phase and noble gas matrix experimental data. We assessed the performance of fifteen functionals and five basis sets for reproducing (i) vibrationless electronic excitation energies and (ii) vibrational frequencies in the singlet excited states. We found that the basis sets of at least triple-ζ quality were necessary to describe the long molecules with alternate single and triple bonds. Vibrational frequency scaling factors are similar for the ground and excited states. The benchmarked spectroscopic parameters were shown to be acceptably reproduced with adequately chosen functionals, in particular ωB97X, CAM-B3LYP, B3LYP, B971, and B972. Select functionals were applied to study the electronic excitation of molecules up to HC₂₇N and C₃₀N₂. It is demonstrated that optical excitation leads to a shift from the polyyne- to a cumulene-like electronic structure. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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15 pages, 3110 KiB

Open AccessArticle

Photo-Induced Reactions between Glyoxal and Hydroxylamine in Cryogenic Matrices

by Barbara Golec, Magdalena Sałdyka and Zofia Mielke

Molecules 2022, 27(15), 4797; https://doi.org/10.3390/molecules27154797 - 27 Jul 2022

Viewed by 1672

Abstract

In this paper, the photochemistry of glyoxal–hydroxylamine (Gly–HA) complexes is studied using FTIR matrix isolation spectroscopy and ab initio calculations. The irradiation of the Gly–HA complexes with the filtered output of a mercury lamp (λ > 370 nm) leads to their photoconversion to hydroxyketene–hydroxylamine complexes and the formation of hydroxy(hydroxyamino)acetaldehyde with a hemiaminal structure. The first product is the result of a double hydrogen exchange reaction between the aldehyde group of Gly and the amino or hydroxyl group of HA. The second product is formed as a result of the addition of the nitrogen atom of HA to the carbon atom of one aldehyde group of Gly, followed by the migration of the hydrogen atom from the amino group of hydroxylamine to the oxygen atom of the carbonyl group of glyoxal. The identification of the products is confirmed by deuterium substitution and by MP2 calculations of the structures and vibrational spectra of the identified species. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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18 pages, 4905 KiB

Open AccessFeature PaperArticle

Structure, Spectra and Photochemistry of 2-Amino-4-Methylthiazole: FTIR Matrix Isolation and Theoretical Studies

by Magdalena Pagacz-Kostrzewa, Daria Bumażnik, Stéphane Coussan and Magdalena Sałdyka

Molecules 2022, 27(12), 3897; https://doi.org/10.3390/molecules27123897 - 17 Jun 2022

Cited by 4 | Viewed by 1949

Abstract

The structure, tautomerization pathways, vibrational spectra, and photochemistry of 2-amino-4-methylthiazole (AMT) molecule were studied by matrix isolation FTIR spectroscopy and DFT calculations undertaken at the B3LYP/6-311++G(3df,3pd) level of theory. The most stable tautomer with the five-membered ring stabilized by two double C=C and C=N bonds, was detected in argon matrices after deposition. When the AMT/Ar matrices were exposed to 265 nm selective irradiation, three main photoproducts, N-(1-sulfanylprop-1-en-2-yl)carbodiimide (fp1), N-(1-thioxopropan-2-yl)carbodiimide (fp2) and N-(2-methylthiiran-2-yl)carbodiimide (fp3), were photoproduced by a cleavage of the CS–CN bond together with hydrogen atom migration. The minor photoreaction caused by the cleavage of the CS–CC bond and followed by hydrogen migration formed 2-methyl-1H-azirene-1-carbimidothioic acid (fp15). We have also found that cleavage of the CS–CN bond followed by disruption of the N–C bond produced cyanamide (fp11) and the C(CH3)=CH–S biradical that transformed into 2-methylthiirene (fp12) and further photoreactions produced 1-propyne-1-thiole (fp13) or methylthioketene (fp14). Cleavage of the CS–CC bond followed by disruption of the N–C bond produced propyne (fp22) and the S–C(NH₂)=N biradical that transformed into 3-aminethiazirene (fp23); further photoreactions produced N-sulfanylcarbodiimide (fp25). As a result of these transformations, several molecular complexes were identified as photoproducts besides new molecules in the AMT photolysis process. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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19 pages, 3514 KiB

Open AccessFeature PaperArticle

Diclofenac Ion Hydration: Experimental and Theoretical Search for Anion Pairs

by Anastasia V. Shishkina, Alexander A. Ksenofontov, Nikita V. Penkov and Mikhail V. Vener

Molecules 2022, 27(10), 3350; https://doi.org/10.3390/molecules27103350 - 23 May 2022

Cited by 8 | Viewed by 3177

Abstract

Self-assembly of organic ions in aqueous solutions is a hot topic at the present time, and substances that are well-soluble in water are usually studied. In this work, aqueous solutions of sodium diclofenac are investigated, which, like most medicinal compounds, is poorly soluble in water. Classical MD modeling of an aqueous solution of diclofenac sodium showed equilibrium between the hydrated anion and the hydrated dimer of the diclofenac anion. The assignment and interpretation of the bands in the UV, NIR, and IR spectra are based on DFT calculations in the discrete-continuum approximation. It has been shown that the combined use of spectroscopic methods in various frequency ranges with classical MD simulations and DFT calculations provides valuable information on the association processes of medical compounds in aqueous solutions. Additionally, such a combined application of experimental and calculation methods allowed us to put forward a hypothesis about the mechanism of the effect of diclofenac sodium in high dilutions on a solution of diclofenac sodium. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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19 pages, 10583 KiB

Open AccessArticle

Spectral Signatures of Hydrogen Thioperoxide (HOSH) and Hydrogen Persulfide (HSSH): Possible Molecular Sulfur Sinks in the Dense ISM

by Charles Z. Palmer, Ryan C. Fortenberry and Joseph S. Francisco

Molecules 2022, 27(10), 3200; https://doi.org/10.3390/molecules27103200 - 17 May 2022

Cited by 4 | Viewed by 2822

Abstract

For decades, sulfur has remained underdetected in molecular form within the dense interstellar medium (ISM), and somewhere a molecular sulfur sink exists where it may be hiding. With the discovery of hydrogen peroxide (HOOH) in the ISM in 2011, a natural starting point may be found in sulfur-bearing analogs that are chemically similar to HOOH: hydrogen thioperoxide (HOSH) and hydrogen persulfide (HSSH). The present theoretical study couples the accuracy in the anharmonic fundamental vibrational frequencies from the explicitly correlated coupled cluster theory with the accurate rotational constants provided by canonical high-level coupled cluster theory to produce rovibrational spectra for use in the potential observation of HOSH and HSSH. The

ν_{6}

mode for HSSH at 886.1 cm

^{- 1}

is within 0.2 cm

^{- 1}

of the gas-phase experiment, and the

B_{0}

rotational constant for HSSH of 6979.5 MHz is within 9.0 MHz of the experimental benchmarks, implying that the unknown spectral features (such as the first overtones and combination bands) provided herein are similarly accurate. Notably, a previous experimentally-attributed 2

ν_{1}

mode, at 7041.8 cm

^{- 1}

, has been reassigned to the

ν_{1} + ν_{5}

combination band based on the present work’s

ν_{1} + ν_{5}

value at 7034.3 cm

^{- 1}

. The most intense vibrational transitions for each molecule are the torsions, with HOSH having a more intense transition of 72 km/mol compared to HSSH’s intensity of 14 km/mol. Furthermore, HOSH has a larger net dipole moment of 1.60 D compared to HSSH’s 1.15 D. While HOSH may be the more likely candidate of the two for possible astronomical observation via vibrational spectroscopy due to the notable difference in their intensities, both HSSH and HOSH have large enough net dipole moments to be detectable by rotational spectroscopy to discover the role these molecules may have as possible molecular sulfur sinks in the dense ISM. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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Review

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34 pages, 17556 KiB

Open AccessReview

Organophosphorus Azoles Incorporating a Tetra-, Penta-, and Hexacoordinated Phosphorus Atom: NMR Spectroscopy and Quantum Chemistry

by Lyudmila Larina

Molecules 2023, 28(2), 669; https://doi.org/10.3390/molecules28020669 - 9 Jan 2023

Cited by 2 | Viewed by 1547

Abstract

The review presents extensive data (from the author’s work and the literature) on the stereochemical structure of functionalized organophosphorus azoles (pyrroles, pyrazoles, imidazoles and benzazoles) and related compounds, using multinuclear ¹H, ¹³C, ³¹P NMR spectroscopy and quantum chemistry. ³¹P NMR spectroscopy, combined with high-level quantum-chemical calculations, is the most convenient and reliable approach to studying tetra-, penta-, and hexacoordinated phosphorus atoms of phosphorylated N-vinylazoles and evaluating their Z/E isomerization. Full article

(This article belongs to the Special Issue Advances in Computational Spectroscopy)

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