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A Special Issue in Honor of Professor Josef Michl

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A special issue of Chemistry (ISSN 2624-8549). This special issue belongs to the section "Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 40032

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Prof. Dr. Igor Alabugin

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Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
Interests: organic reaction mechanisms; stereoelectronic effects; organic photochemistry; DNA photocleavage; carbon-rich materials; chemistry of alkynes; radical chemistry; cyclizations; cycloaromatizations; electron upconversion; hole catalysis; high energy functional groups
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Prof. Dr. Petr Klán

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Department of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Brno, Czech Republic
Interests: organic photochemistry; mechanistic photochemistry; time-resolved spectroscopy; photoactivatable compounds; photorelease of small molecules; fluorescent probes; environmental photochemistry

Special Issue Information

Dear Colleagues,

This Special Issue of Chemistry is dedicated to Professor Josef Michl, a pioneer in several theoretical and experimental fields of chemistry. After obtaining a Ph.D. degree at Czechoslovak Academy of Sciences, Prague, Czechoslovakia, in 1965 and working as a postdoctoral fellow at the University of Houston and the University of Texas at Austin, he was associated with several institutions, including the Aarhus University, the University of Utah, and the University of Texas at Austin. Currently, he works at the University of Colorado Boulder, USA, and the Institute of Organic Chemistry and Biochemistry at the Czech Academy of Sciences, Prague, Czech Republic. He has made significant contributions to many fields of theoretical and experimental organic chemistry, such as organic photochemistry, chemistry of biradicals and biradicaloids, electronic and vibrational spectroscopy, silicon and boron chemistry, reactive intermediates, and magnetic circular dichroism.

This Special Issue will have a broad focus on mechanistic aspects of organic/inorganic chemistry, including photochemistry; reactive intermediates; molecular rotors; fluorine, silicon, and boron chemistry; organometallics; and some others.

Prof. Dr. Igor Alabugin
Prof. Dr. Petr Klán
Guest Editors

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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. Chemistry is an international peer-reviewed open access semimonthly journal published by MDPI.

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Published Papers (13 papers)

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Editorial

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2 pages, 193 KiB

Open AccessEditorial

A Special Issue in Honor of Professor Josef Michl

by Igor Alabugin and Petr Klán

Chemistry 2022, 4(2), 270-271; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry4020021 - 30 Mar 2022

Viewed by 1352

Abstract

This Special Issue of Chemistry is dedicated to Professor Josef Michl [...] Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

4 pages, 1505 KiB

Open AccessEditorial

Tribute to Josef Michl

by Igor Alabugin and Petr Klán

Chemistry 2021, 3(1), 440-443; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010032 - 22 Mar 2021

Cited by 1 | Viewed by 2822

Abstract

It is our great pleasure to introduce the Festschrift of Chemistry to honor professor Josef Michl (Figure 1) on the occasion of his 80th birthday and to recognize his exceptional contributions to the fields of organic photochemistry, quantum chemistry, biradicals and biradicaloids, electronic and vibrational spectroscopy, magnetic circular dichroism, silicon and boron chemistry, supramolecular chemistry, singlet fission, and molecular machines [...] Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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Research

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11 pages, 3703 KiB

Open AccessArticle

Solvation Effects on the Thermal Helix Inversion of Molecular Motors from QM/MM Calculations

by Jin Wen, Meifang Zhu and Leticia González

Chemistry 2022, 4(1), 185-195; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry4010016 - 15 Mar 2022

Cited by 5 | Viewed by 2292

Abstract

Molecular motors convert light and thermal energies into mechanical work, offering good opportunities to design novel molecular devices. Among them, molecular motors alternate a photoisomerization and a thermal helix inversion to achieve unidirectional rotation. The rotational speed is limited by the helix inversion step, which in turn is governed by a barrier in the electronic ground state. In this work, we systematically study the solvation effect on the thermal process of selected molecular motors, comparing reaction barriers obtained from both density functional theory (DFT) in the isolated system and umbrella sampling within a hybrid quantum mechanics/molecular mechanics (QM/MM) model in solution. We find more prominent solvation effects on those molecular motors with larger dipole moments. The results could provide insight into how to functionalize molecular motors to speed up their rotation. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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9 pages, 1227 KiB

Open AccessArticle

Light-Induced Charge Accumulation in PTCDI/Pentacene/Ag(111) Heterojunctions

by Roberto Costantini, Albano Cossaro, Alberto Morgante and Martina Dell’Angela

Chemistry 2021, 3(3), 744-752; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3030053 - 13 Jul 2021

Cited by 1 | Viewed by 2375

Abstract

The incorporation of singlet fission (SF) chromophores in solar cells is expected to bring significant increases in the power conversion efficiency thanks to multiexciton generation. However, efficient charge generation in the device is determined by the energy level alignment (ELA) between the active materials, which should favor exciton transport and separation under illumination. By combining ultraviolet photoemission spectroscopy and optical differential reflectance measurements, we determine the ELA in a prototypical SF heterojunction between pentacene (Pc) and perylene-tetracarboxylic-diimide (PTCDI) grown on Ag(111). Time-resolved X-ray photoelectron spectroscopy on such a system reveals light-induced modifications of the ELA; by measuring the transient shift of the core level photoemission lines we observe an accumulation of long-lived holes in the PTCDI within the first hundred picoseconds after the optical pump. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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18 pages, 5943 KiB

Open AccessFeature PaperArticle

Exploitation of Baird Aromaticity and Clar’s Rule for Tuning the Triplet Energies of Polycyclic Aromatic Hydrocarbons

by Felix Plasser

Chemistry 2021, 3(2), 532-549; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020038 - 14 Apr 2021

Cited by 15 | Viewed by 4184

Abstract

Polycyclic aromatic hydrocarbons (PAH) are a prominent substance class with a variety of applications in molecular materials science. Their electronic properties crucially depend on the bond topology in ways that are often highly non-intuitive. Here, we study, using density functional theory, the triplet states of four biphenylene-derived PAHs finding dramatically different triplet excitation energies for closely related isomeric structures. These differences are rationalised using a qualitative description of Clar sextets and Baird quartets, quantified in terms of nucleus independent chemical shifts, and represented graphically through a recently developed method for visualising chemical shielding tensors (VIST). The results are further interpreted in terms of a 2D rigid rotor model of aromaticity and through an analysis of the natural transition orbitals involved in the triplet excited states showing good consistency between the different viewpoints. We believe that this work constitutes an important step in consolidating these varying viewpoints of electronically excited states. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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18 pages, 1912 KiB

Open AccessFeature PaperArticle

Effects of Substituents on Photophysical and CO-Photoreleasing Properties of 2,6-Substituted meso-Carboxy BODIPY Derivatives

by Esther M. Sánchez-Carnerero, Marina Russo, Andreas Jakob, Lucie Muchová, Libor Vítek and Petr Klán

Chemistry 2021, 3(1), 238-255; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010018 - 09 Feb 2021

Cited by 7 | Viewed by 3258

Abstract

Carbon monoxide (CO) is an endogenously produced signaling molecule involved in the control of a vast array of physiological processes. One of the strategies to administer therapeutic amounts of CO is the precise spatial and temporal control over its release from photoactivatable CO-releasing molecules (photoCORMs). Here we present the synthesis and photophysical and photochemical properties of a small library of meso-carboxy BODIPY derivatives bearing different substituents at positions 2 and 6. We show that the nature of substituents has a major impact on both their photophysics and the efficiency of CO photorelease. CO was found to be efficiently released from π-extended 2,6-arylethynyl BODIPY derivatives possessing absorption spectra shifted to a more biologically desirable wavelength range. Selected photoCORMs were subjected to in vitro experiments that did not reveal any serious toxic effects, suggesting their potential for further biological research. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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10 pages, 2387 KiB

Open AccessFeature PaperArticle

Exchange Speed of Four-Component Nanorotors Correlates with Hammett Substituent Constants

by Yi-Fan Li, Amit Ghosh, Pronay Kumar Biswas, Suchismita Saha and Michael Schmittel

Chemistry 2021, 3(1), 116-125; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010009 - 22 Jan 2021

Cited by 3 | Viewed by 2339

Abstract

Three distinct four-component supramolecular nanorotors were prepared, using, for the first time, bipyridine instead of phenanthroline stations in the stator. Following our established self-sorting protocol to multicomponent nanodevices, the nanorotors were self-assembled by mixing the stator, rotators with various pyridine head groups, copper(I) ions and 1,4-diazabicyclo[2.2.2]octane (DABCO). Whereas the exchange of a phenanthroline vs. a bipyridine station did not entail significant changes in the rotational exchange frequency, the para-substituents at the pyridine head group of the rotator had drastic consequences on the speed: 4-OMe (k₂₉₈ = 35 kHz), 4-H (k₂₉₈ = 77 kHz) and 4-NO₂ (k₂₉₈ = 843 kHz). The exchange frequency (log k) showed an excellent linear correlation with both the Hammett substituent constants and log K of the copper(I)–ligand interaction, proving that rotator–copper(I) bond cleavage is the key determining factor in the rate-determining step. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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12 pages, 12741 KiB

Open AccessArticle

Synthesis and Photostability of Cyclooctatetraene-Substituted Free Base Porphyrins

by Joanna Buczyńska, Agnieszka Gajewska, Aleksander Gorski, Barbara Golec, Krzysztof Nawara, Renata Rybakiewicz and Jacek Waluk

Chemistry 2021, 3(1), 104-115; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010008 - 21 Jan 2021

Cited by 3 | Viewed by 2936

Abstract

A series of free base meso-tetraarylporphyrins functionalized with substituents containing one, two, and four cyclooctatetraene (COT) moieties have been obtained and characterized by spectral and photophysical studies. Three COT-free porphyrins served as reference compounds. COT is a triplet quencher, well-known to enhance the photostability of several, but not all, fluorophores. In the case of porphyrins, substitution with COT improves photostability in zinc derivatives, but for free bases, the effect is the opposite. We show that placing the COT moiety further from the free base porphyrin core enhances the photostability when the COT group lies in the direct vicinity of the macrocycle. The quantum yields of photobleaching inversely correlate with porphyrin oxidation potentials. An improvement in photostability in both COT-containing and COT-free porphyrins can be achieved by screening the porphyrin core from oxygen by switching from tolyl to mesityl substituents. This leads to a decrease in the photobleaching quantum yield, even though triplet lifetimes are longer. The results confirm the involvement of oxygen in the photodegradation of porphyrins. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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10 pages, 2730 KiB

Open AccessArticle

Lattice Dynamics of KAgF₃ Perovskite, Unique 1D Antiferromagnet

by Kacper Koteras, Jakub Gawraczyński, Mariana Derzsi, Zoran Mazej and Wojciech Grochala

Chemistry 2021, 3(1), 94-103; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010007 - 19 Jan 2021

Cited by 7 | Viewed by 2279

Abstract

Theoretical DFT calculations using GGA+U and HSE06 frameworks enabled vibrational mode assignment and partial (atomic) phonon DOS determination in KAgF₃ perovskite, a low-dimensional magnetic fluoroargentate(II). Twelve bands in the spectra of KAgF₃ were assigned to either IR active or Raman active modes, reaching excellent correlation with experimental values (R2 > 0.997). Low-temperature Raman measurements indicate that the intriguing spin-Peierls-like phase transition at 230 K is an order–disorder transition and it does not strongly impact the vibrational structure of the material. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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6 pages, 8161 KiB

Open AccessCommunication

Solid-State ²H NMR Study for Deuterated Phenylene Dynamics in a Crystalline Gyroscope-Like Molecule

by Wataru Setaka, Kentaro Yamaguchi and Mitsuo Kira

Chemistry 2021, 3(1), 39-44; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010004 - 07 Jan 2021

Cited by 2 | Viewed by 2045

Abstract

Molecular rotors have earned substantial popularity in recent times, owing to the unique dependence of its crystalline properties on the rotational dynamics of the rotor. We have recently reported the synthesis and crystal structure of a phenylene-bridged macrocage as a gyroscope-like molecule in the crystalline state. The dynamics of the phenylene moiety was probed by solid-state ¹³C CP/MAS proton dipolar dephasing NMR spectroscopy. Herein, solid-state ²H NMR studies were performed to study the dynamics of the gyroscope-like molecule with a deuterated rotor in the crystalline state. A spectrum with a narrow line shape was obtained at 300 K. The facile exchange among three stationary states, which was observed by X-ray crystallography, was clearly confirmed. Additionally, a crystal-to-crystal phase transition that switches the motion of the rotor was observed in the DSC analysis of the powdered sample. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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11 pages, 2891 KiB

Open AccessArticle

On the 3D → 2D Isomerization of Hexaborane(12)

by Josep M. Oliva-Enrich, Ibon Alkorta, José Elguero, Maxime Ferrer and José I. Burgos

Chemistry 2021, 3(1), 28-38; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010003 - 01 Jan 2021

Cited by 4 | Viewed by 3141

Abstract

By following the intrinsic reaction coordinate connecting transition states with energy minima on the potential energy surface, we have determined the reaction steps connecting three-dimensional hexaborane(12) with unknown planar two-dimensional hexaborane(12). In an effort to predict the potential synthesis of finite planar borane molecules, we found that the reaction limiting factor stems from the breaking of the central boron-boron bond perpendicular to the C₂ axis of rotation in three-dimensional hexaborane(12). Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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15 pages, 6914 KiB

Open AccessArticle

Kinetic Stability of Si₂C₅H₂ Isomer with a Planar Tetracoordinate Carbon Atom

by Krishnan Thirumoorthy, Vijayanand Chandrasekaran, Andrew L. Cooksy and Venkatesan S. Thimmakondu

Chemistry 2021, 3(1), 13-27; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3010002 - 31 Dec 2020

Cited by 15 | Viewed by 3575

Abstract

Dissociation pathways of the global minimum geometry of Si

_{2}

_{5}

_{2}

with a planar tetracoordinate carbon (ptC) atom, 2,7-disilatricyclo[4.1.0.0

^{1, 3}

]hept-2,4,6-trien-2,7-diyl (1), have been theoretically investigated using density functional theory and coupled-cluster (CC) methods. Dissociation of [...] Read more.

Dissociation pathways of the global minimum geometry of Si

_{2}

_{5}

_{2}

with a planar tetracoordinate carbon (ptC) atom, 2,7-disilatricyclo[4.1.0.0

^{1, 3}

]hept-2,4,6-trien-2,7-diyl (1), have been theoretically investigated using density functional theory and coupled-cluster (CC) methods. Dissociation of Si-C bond connected to the ptC atom leads to the formation of 4,7-disilabicyclo[4.1.0]hept-1(6),4(5)-dien-2-yn-7-ylidene (4) through a single transition state. Dissociation of C-C bond connected to the ptC atom leads to an intermediate with two identical transition states and leads back to 1 itself. Simultaneous breaking of both Si-C and C-C bonds leads to an acyclic transition state, which forms an acyclic product, cis-1,7-disilahept-1,2,3,5,6-pentaen-1,7-diylidene (19). Overall, two different products, four transition states, and an intermediate have been identified at the B3LYP/6-311++G(2d,2p) level of theory. Intrinsic reaction coordinate calculations have also been done at the latter level to confirm the isomerization pathways. CC calculations have been done at the CCSD(T)/cc-pVTZ level of theory for all minima. Importantly, all reaction profiles for 1 are found be endothermic in Si

_{2}

_{5}

_{2}

. These results are in stark contrast compared to the structurally similar and isovalent lowest-energy isomer of C

_{7}

_{2}

with a ptC atom as the overall reaction profiles there have been found to be exothermic. The activation energies for Si-C, C-C, and Si-C/C-C breaking are found to be 30.51, 64.05, and 61.85 kcal mol

^{- 1}

, respectively. Thus, it is emphasized here that 1 is a kinetically stable molecule. However, it remains elusive in the laboratory to date. Therefore, energetic and spectroscopic parameters have been documented here, which may be of relevance to molecular spectroscopists in identifying this key anti-van’t-Hoff-Le Bel molecule. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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20 pages, 5439 KiB

Open AccessArticle

The Photophysical Properties of Triisopropylsilyl-ethynylpentacene—A Molecule with an Unusually Large Singlet-Triplet Energy Gap—In Solution and Solid Phases

by Fabio A. Schaberle, Carlos Serpa, Luis G. Arnaut, Andrew D. Ward, Joshua K. G. Karlsson, Alparslan Atahan and Anthony Harriman

Chemistry 2020, 2(2), 545-564; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry2020033 - 03 Jun 2020

Cited by 14 | Viewed by 4435

Abstract

The process of singlet-exciton fission (SEF) has attracted much attention of late. One of the most popular SEF compounds is TIPS-pentacene (TIPS-P, where TIPS = triisopropylsilylethynyl) but, despite its extensive use as both a reference and building block, its photophysical properties are not so well established. In particular, the triplet state excitation energy remains uncertain. Here, we report quantitative data and spectral characterization for excited-singlet and -triplet states in dilute solution. The triplet energy is determined to be 7940 ± 1200 cm⁻¹ on the basis of sensitization studies using time-resolved photoacoustic calorimetry. The triplet quantum yield at the limit of low concentration and low laser intensity is only ca. 1%. Self-quenching occurs at high solute concentration where the fluorescence yield and lifetime decrease markedly relative to dilute solution but we were unable to detect excimer emission by steady-state spectroscopy. Short-lived fluorescence, free from excimer emission or phosphorescence, occurs for crystals of TIPS-P, most likely from amorphous domains. Full article

(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)

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