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Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 19605

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Prof. Dr. Georgiy Girichev

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Guest Editor

Nanomaterial Research Institute, Ivanovo State University, 153025 Ivanovo, Russia
Interests: molecular structure; intramolecular dynamics; thermodynamics, IR spectra; gas-phase electron diffraction; mass spectrometry; DFT and ab initio calculations
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

The dialectic of the development of science is expressed in the fact that today's experiment must give way to tomorrow's theory, which makes this experiment unnecessary, but which, in turn, must give way to a new, more accurate experiment the day after tomorrow, and so on.

The problem along this path is the different physical meaning of the molecular parameters obtained in experiment and in quantum chemical calculations.

The experimental data refer to a real object. The structural parameters, obtained by diffraction methods, are averaged over electronic, vibrational, and rotational levels populated under the experimental conditions, or bear the imprint of collective interaction. The latter often manifests itself in the results of many spectroscopic studies.

At the same time, the structural and spectroscopic parameters obtained in routine quantum chemical calculations refer to the unobservable hypothetical equilibrium structure of the molecule.

In this regard, the problem of comparing and mutually complementing the experimental and calculated data arises, and the solution of this problem requires further development.

We are pleased to invite you to present your works in this Special Issue, which considers examples of the joint use of experimental and calculated data and the problems that arise in this connection.

Prof. Dr. Georgiy V. Girichev
Guest Editor

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Keywords

molecular structure
nature of chemical bonding
IR spectra
EA spectra
NMR
XRD
DFT
ab initio

Published Papers (13 papers)

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Research

14 pages, 3144 KiB

Open AccessArticle

Photoprocesses in Derivatives of 1,4- and 1,3-Diazadistyryldibenzenes

by Levon S. Atabekyan, Alexandra Y. Freidzon, Dmitry S. Ionov, Vyacheslav N. Nuriev, Alexey V. Medved’ko, Sergey Z. Vatsadze, Sergey P. Gromov and Alexander K. Chibisov

Int. J. Mol. Sci. 2022, 23(23), 15346; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232315346 - 05 Dec 2022

Viewed by 1014

Abstract

Photoprocesses in 1,4-diazadistyrylbenzene (1) and 1,3-diazadistyrylbenzene derivative (2) diperchlorates in MeCN were studied by absorption, luminescence, and kinetic laser spectroscopies. For compound 1, trans-cis-photoisomerization and intersystem crossing to a triplet state are observed. For compound 2, photoelectrocyclization is suggested. Quantum chemical calculations of diazadistyrylbenzene structures in the ground and excited states were carried out. The schemes for photoreactions were proposed. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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13 pages, 1603 KiB

Open AccessArticle

Cyclic Dimers of 4-n-Propyloxybenzoic Acid with Hydrogen Bonds in the Gaseous State

by Nina I. Giricheva, Ksenia E. Bubnova, Alexander V. Krasnov and Georgiy V. Girichev

Int. J. Mol. Sci. 2022, 23(23), 15079; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232315079 - 01 Dec 2022

Cited by 2 | Viewed by 908

Abstract

A comprehensive study of saturated vapors of 4-n-propyloxybenzoic acid (POBA) by gas electron diffraction (GED) and mass spectrometric (MS) methods supplemented by quantum chemical (QC) calculations was carried out for the first time. An attempt was made to detect dimeric forms of the acid in the gaseous state. It has been established that at the temperature of GED experiment, vapor over a solid sample contains up to 20 mol.% of cyclic dimers with two O-H...O hydrogen bonds. The main geometrical parameters of gaseous monomers and dimers of POBA are obtained. The distance r(O…O) = 2.574(12) Å in the cyclic fragment of the gaseous dimer is close to that in the crystal structure (2.611 Å). In the mass spectrum of the POBA recorded the ions of low intensity with a mass exceeding the molecular mass of the monomer were detected. The presence of ions, whose elemental composition corresponds to the dissociative ionization of the dimer, confirms the results of the GED experiment on the presence of POBA dimers in the gas state. The results of GED studies of acetic acid, benzoic acid, and POBA were compared. It is shown that the COOH fragment saves its geometric structure in monomers, as well as the COOH...HOOC fragment with two hydrogen bonds in dimers of different acids. The intermolecular interaction energy in considered acid dimers was estimated using QC calculations (B97D/6-311++G **). The significant value of last (>84 kJ/mol) is the reason for the noticeable presence of dimers in the gas phase. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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20 pages, 3453 KiB

Open AccessArticle

Nature of Beryllium, Magnesium, and Zinc Bonds in Carbene⋯MX₂ (M = Be, Mg, Zn; X = H, Br) Dimers Revealed by the IQA, ETS-NOCV and LED Methods

by Filip Sagan, Mariusz Mitoraj and Mirosław Jabłoński

Int. J. Mol. Sci. 2022, 23(23), 14668; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232314668 - 24 Nov 2022

Cited by 2 | Viewed by 1588

Abstract

The nature of beryllium–, magnesium– and zinc–carbene bonds in the cyclopropenylidene⋯MX

_{2}

(M = Be, Mg, Zn; X = H, Br) and imidazol-2-ylidene⋯MBr

_{2}

dimers is investigated by the joint use of the topological QTAIM-based IQA decomposition scheme, the molecular orbital-based ETS-NOCV charge [...] Read more.

The nature of beryllium–, magnesium– and zinc–carbene bonds in the cyclopropenylidene⋯MX

_{2}

(M = Be, Mg, Zn; X = H, Br) and imidazol-2-ylidene⋯MBr

_{2}

dimers is investigated by the joint use of the topological QTAIM-based IQA decomposition scheme, the molecular orbital-based ETS-NOCV charge and energy decomposition method, and the LED energy decomposition approach based on the state-of-the-art DLPNO-CCSD(T) method. All these methods show that the C⋯M bond strengthens according to the following order: Zn < Mg

< <

Be. Electrostatics is proved to be the dominant bond component, whereas the orbital component is far less important. It is shown that QTAIM/IQA underestimates electrostatic contribution for zinc bonds with respect to both ETS-NOCV and LED schemes. The

σ

carbene→MX

_{2}

donation appears to be much more important than the MX

_{2} \to

carbene back-donation of

π

symmetry. The substitution of hydrogen atoms by bromine (X in MX

_{2}

) strengthens the metal–carbene bond in all cases. The physical origin of rotational barriers has been unveiled by the ETS-NOCV approach. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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15 pages, 3616 KiB

Open AccessArticle

Molecular Structure, Vibrational Spectrum and Conformational Properties of 4-(4-Tritylphenoxy)phthalonitrile-Precursor for Synthesis of Phthalocyanines with Bulky Substituent

by Natalia V. Tverdova, Nina I. Giricheva, Vladimir E. Maizlish, Nikolay E. Galanin and Georgiy V. Girichev

Int. J. Mol. Sci. 2022, 23(22), 13922; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232213922 - 11 Nov 2022

Cited by 3 | Viewed by 1006

Abstract

By DFT method with B3LYP, PBE, CAM-B3LYP, and B97D functionals, it was found that the molecule 4-(4-tritylphenoxy)phthalonitrile (TPPN) has four conformers. The geometric structure, vibrational frequencies, electronic characteristics, and thermodynamic functions of conformers, as well as the structure and energy of transition states, were determined. IR spectrum of TPPN film contains vibrational bands belonging to different conformers. The assignment of bands was performed basing the distribution of normal vibration energy on internal coordinates. A synchronous electron diffraction/mass spectrometric experiment was performed to determine the structure of conformers in a saturated TPPN vapor. The elemental composition of the ions recorded in the mass spectrum indicates the thermal stability of TPPN at least up to T = 200 °C. The difference in the structure of tetrasubstituted metal phthalocyanines, which can be synthesized from different TPPN conformers, has been shown. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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12 pages, 2365 KiB

Open AccessArticle

Spin-Crossover and Slow Magnetic Relaxation Behavior in Hexachlororhenate(IV) Salts of Mn(III) Complexes [Mn(5-Hal-sal₂323)]₂[ReCl₆] (Hal = Cl, Br)

by Aleksandra V. Tiunova, Anna V. Kazakova, Denis V. Korchagin, Gennady V. Shilov, Sergey M. Aldoshin, Aleksei I. Dmitriev, Mikhail V. Zhidkov, Konstantin V. Zakharov and Eduard B. Yagubskii

Int. J. Mol. Sci. 2022, 23(19), 11449; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911449 - 28 Sep 2022

Cited by 4 | Viewed by 1300

Abstract

The cationic complexes of Mn(III) with the 5-Hal-sal₂323 (Hal = Cl, Br) ligands and a paramagnetic doubly charged counterion [ReCl₆]²⁻ have been synthesized: [Mn(5-Cl-sal₂323)]₂[ReCl₆] (1) and [Mn(5-Br-sal₂323)]₂[ReCl₆] (2). Their crystal structures and magnetic properties have been studied. These isostructural two-component ionic compounds show a thermally induced spin transition at high temperature associated with the cationic subsystem and a field-induced slow magnetic relaxation of magnetization at cryogenic temperature, associated with the anionic subsystem. The compounds are the first examples of the coexistence of spin crossover and field-induced slow magnetic relaxation in the family of known [Mn^III(sal₂323)] cationic complexes with various counterions. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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16 pages, 2637 KiB

Open AccessCommunication

How Do Intermolecular Interactions Evolve at the Nematic to Twist–Bent Phase Transition?

by Katarzyna Merkel, Barbara Loska, Yuki Arakawa, Georg H. Mehl, Jakub Karcz and Antoni Kocot

Int. J. Mol. Sci. 2022, 23(19), 11018; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911018 - 20 Sep 2022

Cited by 4 | Viewed by 1243

Abstract

Polarized beam infrared (IR) spectroscopy provides valuable information on changes in the orientation of samples in nematic phases, especially on the role of intermolecular interactions in forming the periodically modulated twist–bent phase. Infrared absorbance measurements and quantum chemistry calculations based on the density functional theory (DFT) were performed to investigate the structure and how the molecules interact in the nematic (N) and twist–bend (N_TB) phases of thioether dimers. The nematic twist–bend phase observed significant changes in the mean IR absorbance. On cooling, the transition from the N phase to the N_TB phase was found to be accompanied by a marked decrease in absorbance for longitudinal dipoles. Then, with further cooling, the absorbance of the transverse dipoles increased, indicating that transverse dipoles became correlated in parallel. To investigate the influence of the closest neighbors, DFT calculations were performed. As a result of the optimization of the molecular cores system, we observed changes in the square of the transition dipoles, which well corresponds to absorbance changes observed in the IR spectra. Interactions of molecules dominated by pairing were observed, as well as the axial shift of the core to each other. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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19 pages, 5727 KiB

Open AccessArticle

New Organic–Inorganic Salt Based on Fluconazole Drug: TD-DFT Benchmark and Computational Insights into Halogen Substitution

by Hela Ferjani, Rim Bechaieb, Marzook Alshammari, O. M. Lemine and Necmi Dege

Int. J. Mol. Sci. 2022, 23(15), 8765; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158765 - 06 Aug 2022

Cited by 9 | Viewed by 2061

Abstract

In this study, we report the synthesis of a new organic–inorganic molecular salt of the clinically used antifungal drug fluconazole, (H2Fluconazole).SnCl₆.2H₂O. By detailed investigation and analysis of its structural properties, we show that the structure represents a 0D structure built of alternating organic and inorganic zig-zag layers along the crystallographic c-axis and the primary supramolecular synthons in this salt are hydrogen bonding, F···π and halogen bonding interactions. Magnetic measurements reveal the co-existence of weak ferromagnetic behavior at low magnetic field and large diamagnetic contributions, indicating that the synthesized material behaves mainly as a diamagnetic material, with very low magnetic susceptibility and with a band gap energy of 3.6 eV, and the salt is suitable for semiconducting applications. Extensive theoretical study is performed to explain the acceptor donor reactivity of this compound and to predict the Cl-substitution effect by F, Br and I. The energy gap, frontier molecular orbitals (FMOs) and the different chemical reactivity descriptors were evaluated at a high theoretical level. Calculations show that Cl substitution by Br and I generates compounds with more important antioxidant ability and the intramolecular charge transfer linked to the inorganic anion. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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16 pages, 3442 KiB

Open AccessArticle

Study of the Experimental and Simulated Vibrational Spectra Together with Conformational Analysis of Thioether Cyanobiphenyl-Based Liquid Crystal Dimers

by Antoni Kocot, Barbara Loska, Yuki Arakawa, Georg H. Mehl and Katarzyna Merkel

Int. J. Mol. Sci. 2022, 23(14), 8005; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23148005 - 20 Jul 2022

Cited by 2 | Viewed by 1572

Abstract

Infrared spectroscopy (IR) and quantum chemistry calculations that are based on the density functional theory (DFT) have been used to study the structure and molecular interactions of the nematic and twist-bend phases of thioether-linked dimers. Infrared absorbance measurements were conducted in a polarized beam for a homogeneously aligned sample in order to obtain more details about the orientation of the vibrational transition dipole moments. The distributions to investigate the structure and conformation of the molecule dihedral angle were calculated. The calculated spectrum was compared with the experimental infrared spectra and as a result, detailed vibrational assignments are reported. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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12 pages, 7885 KiB

Open AccessArticle

Rashba Splitting and Electronic Valley Characteristics of Janus Sb and Bi Topological Monolayers

by Qi Gong and Guiling Zhang

Int. J. Mol. Sci. 2022, 23(14), 7629; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23147629 - 10 Jul 2022

Cited by 2 | Viewed by 1395

Abstract

Janus Sb and Bi monolayers as a new class of 2D topological insulator materials, which could be fulfilled by asymmetrical functionalizations with methyl or hydroxyl, are demonstrated by first-principles spin–orbit coupling (SOC) electronic structure calculations to conflate nontrivial topology, Rashba splitting and valley-contrast circular dichroism. Cohesive energies and phonon frequency dispersion spectra indicate that all Janus Sb and Bi monolayers possess a structural stability in energetic statics but represent virtual acoustic phonon vibrations of the hydrogen atoms passivating on monolayer surfaces. Band structures of Janus Sb and Bi monolayers and their nanoribbons demonstrate they are nontrivial topological insulators. Rashba spin splitting at G point in Brillouin zone of Janus Bi monolayers arises from the strong SOC p_x and p_y orbitals of Bi bonding atoms together with the internal out-of-plane electric field caused by asymmetrical functionalization. Janus Sb and Bi monolayers render direct and indirect giant bandgaps, respectively, which are derived from the strong SOC p_x and p_y orbitals at band-valley Brillouin points K and K′ where valley-selective circular dichroism of spin valley Hall insulators is also exhibited. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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16 pages, 3206 KiB

Open AccessArticle

DFT Study of Molecular Structure, Electronic and Vibrational Spectra of Tetrapyrazinoporphyrazine, Its Perchlorinated Derivative and Their Al, Ga and In Complexes

by Igor V. Ryzhov, Alexey V. Eroshin, Yuriy A. Zhabanov, Daniil N. Finogenov and Pavel A. Stuzhin

Int. J. Mol. Sci. 2022, 23(10), 5379; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23105379 - 11 May 2022

Cited by 7 | Viewed by 1455

Abstract

Electronic and geometric structures of metal-free, Al, Ga and In complexes with tetrapyrazinoporphyrazine (TPyzPA) and octachlorotetrapyrazinoporphyrazine (TPyzPACl₈) were investigated by density functional theory (DFT) calculations and compared in order to study the effect of chlorination on the structure and properties of these macrocycles. The nature of the bonds between metal atoms and nitrogen atoms was described using the NBO-analysis. Simulation and interpretation of electronic spectra were performed with the use of time-dependent density functional theory (TDDFT). A description of calculated IR spectra was carried out based on the analysis of the distribution of the potential energy of normal vibrational coordinates. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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13 pages, 2091 KiB

Open AccessArticle

Protonation of Borylated Carboxonium Derivative [2,6-B₁₀H₈O₂CCH₃]⁻: Theoretical and Experimental Investigation

by Ilya N. Klyukin, Anastasia V. Kolbunova, Alexander S. Novikov, Aleksey V. Nelyubin, Nikita A. Selivanov, Alexander Yu. Bykov, Alexandra A. Klyukina, Andrey P. Zhdanov, Konstantin Yu. Zhizhin and Nikolay T. Kuznetsov

Int. J. Mol. Sci. 2022, 23(8), 4190; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23084190 - 10 Apr 2022

Cited by 8 | Viewed by 1706

Abstract

The process of protonation of [2,6-B₁₀H₈O₂CCH₃]⁻ was investigated both theoretically and experimentally. The most suitable conditions for protonation of the derivative [2,6-B₁₀H₈O₂CCH₃]⁻ were found. The process of protonation was carried out in the presence of an excess of trifluoromethanesulfonic acid CF₃SO₃H at room temperature in dichloromethane solution. The structure of the resulting complex [2,6-B₁₀H₈O₂CCH₃*H^fac]⁰ was established using NMR data and the results of DFT calculations. An additional proton atom H^fac was found to be localized on one of the facets that was opposite the boron atom in a substituted position, and which bonded mainly with one apical boron atom. The main descriptors of the B-H^fac bond were established theoretically using QTAIM and NBO approaches. In addition, the mechanism of [2,6-B₁₀H₈O₂CCH₃]⁻ protonation was investigated. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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16 pages, 6123 KiB

Open AccessArticle

Vibrational Spectra and Molecular Vibrational Behaviors of Dibenzyl Disulfide, Dibenzyl Sulphide and Bibenzyl

by Ziyi Wang, Ruimin Song, Weigen Chen, Jianxin Wang, Pinyi Wang, Zhixian Zhang, Xinyuan Zhang and Fu Wan

Int. J. Mol. Sci. 2022, 23(4), 1958; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23041958 - 10 Feb 2022

Cited by 9 | Viewed by 1760

Abstract

The vibration spectroscopy (Raman and infrared) of widely concerned molecules in sulfur corrosion phenomenon (Dibenzyl Disulfide, Dibenzyl Sulphide, and Bibenzyl) is detailedly analyzed based on density functional theory and experimental measurement. The dominant conformations of these molecules are determined according to Boltzmann distribution in relative Gibbs free energy. Additionally, noncovalent interaction analysis is conducted to indicate intramolecular interaction. Vibration normal mode is assigned based on potential energy distribution, which comprehensively reveals the molecular vibrational behaviors. Conformations weighted spectra are obtained and compared with experimentally measured spectra. We found that experimental spectra are in good agreement with the theoretical spectra in B3LYP-D3(BJ)/6-311G** level with a frequency correction factor. Furthermore, the divergence among these molecules is discussed. The vibrational behavior of the methylene group in the molecule shows a trend with the presence of the sulfur atom. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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13 pages, 1942 KiB

Open AccessArticle

New Light on an Old Story: Breaking Kasha’s Rule in Phosphorescence Mechanism of Organic Boron Compounds and Molecule Design

by Dan Deng, Bingbing Suo and Wenli Zou

Int. J. Mol. Sci. 2022, 23(2), 876; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23020876 - 14 Jan 2022

Cited by 1 | Viewed by 1568

Abstract

In this work, the phosphorescence mechanism of (E)-3-(((4-nitrophenyl)imino)methyl)-2H-thiochroman-4-olate-BF2 compound (S-BF2) is investigated theoretically. The phosphorescence of S-BF2 has been reassigned to the second triplet state (

T_{2}

) by the density matrix renormalization group (DMRG) method combined with the multi-configurational pair density [...] Read more.

T_{2}

) by the density matrix renormalization group (DMRG) method combined with the multi-configurational pair density functional theory (MCPDFT) to approach the limit of theoretical accuracy. The calculated radiative and non-radiative rate constants support the breakdown of Kasha’s rule further. Our conclusion contradicts previous reports that phosphorescence comes from the first triplet state (

T_{1}

). Based on the revised phosphorescence mechanism, we have purposefully designed some novel compounds in theory to enhance the phosphorescence efficiency from

T_{2}

by replacing substitute groups in S-BF2. Overall, both S-BF2 and newly designed high-efficiency molecules exhibit anti-Kasha

T_{2}

phosphorescence instead of the conventional

T_{1}

emission. This work provides a useful guidance for future design of high-efficiency green-emitting phosphors. Full article

(This article belongs to the Special Issue Molecular Structure, Electronic and Vibrational Spectra Theoretical Calculations in Materials Sciences)

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