Submit to Molecules Review for Molecules Propose a Special Issue

Journal Browser

► Journal Browser

Open-Shell Systems for Functional Materials

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

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

Deadline for manuscript submissions: closed (31 December 2018) | Viewed by 49171

Share This Special Issue

Special Issue Editors

Prof. Dr. Yasutaka Kitagawa

E-Mail Website
Guest Editor

Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
Interests: quantum chemistry; theoretical coordination chemistry; metal complexes; open-shell systems; molecular magnetism; electron conductivity; optical property; chemical reaction; broken-symmetry method; approximate spin-projection method

Prof. Dr. Ryohei Kishi

E-Mail Website
Guest Editor

Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
Interests: quantum chemistry; physical chemistry; electron dynamics; open-shell systems; optical property; organic compounds; broken-symmetry method; excited state calculations

Prof. Dr. Masayoshi Nakano

E-Mail Website
Guest Editor

Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
Interests: quantum chemistry; theoretical chemistry; open-shell systems; aromaticity; nonlienar optical materials; optical property; singlet fission; exciton dynamics; moelcular design; qunatum dissipative dynamics

Special Issue Information

Dear Colleagues,

For a past few decades, many reports about open-shell systems, such as polynuclear metal complexes and anti-aromatic systems, have been actively investigated in the field of chemistry. Those systems usually involve complicated electronic structures that are constructed by metal–metal (d-d), metal–ligands (d-p), p-p interactions, and so on. However, they often bring many interesting and noble physical functionalities, such as magnetism, non-linear optics, electron conductivity, as well as chemical functionalities, such as catalytic and redox properties. In addition, it has been revealed that biological systems utilize open-shell systems, such as the Mn cluster in photosystem II and the 4Fe-4S cluster in electron transfer proteins, by controlling their electronic structures well. In this way, open-shell systems are widely noticed from the viewpoint of fundamental studies on their peculiar characteristics, applications to materials, as well as an understanding of the biological functions. From these reasons, an elucidation of the relationships among electronic structures, molecular structures, and physical properties is currently a quite important subject.

In recent years, on the other hand, direct predictions of such electronic structures, molecular structures, and physical properties of those open-shell systems are fairly realized by progress in computers and computational methods. In this sense, theoretical calculations are now one of the powerful tools for understanding such systems. However, these systems are, in a sense, still challenging subjects because they are usually large and orbitally-degenerated systems with localized electron spins (localized orbitals).

From these points of view, in this Special Issue, we focus on recent developments, advances and future prospects of open-shell systems. We welcome contributions from both experimental and theoretical researchers, as well as cooperative studies between theories and experiments. Topics to be discussed cover a broad range of fields concerning open-shell systems, from basic theory in quantum theory, fundamental material science, applications in functional materials and biosystems, etc. We also welcome the intersectional area between material science and biomolecular science.

Prof. Yasutaka Kitagawa
Prof. Ryohei Kishi
Prof. Masayoshi Nakano
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

Open-shell systems
Orbitally-degenerated systems
Spin-polarized systems
Quantum theory
Fundamental material science
Functional materials
Biosystems

Published Papers (13 papers)

Download All Papers

Research

Jump to: Review

11 pages, 3013 KiB

Open AccessFeature PaperArticle

Theoretical Study on the Difference in Electron Conductivity of a One-Dimensional Penta-Nickel(II) Complex between Anti-Ferromagnetic and Ferromagnetic States—Possibility of Molecular Switch with Open-Shell Molecules

by Yasutaka Kitagawa, Hayato Tada, Iori Era, Takuya Fujii, Kazuki Ikenaga and Masayoshi Nakano

Molecules 2019, 24(10), 1956; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24101956 - 21 May 2019

Cited by 8 | Viewed by 2526

Abstract

The electron conductivity of an extended metal atom chain (EMAC) that consisted of penta-nickel(II) ions bridged by oligo-α-pyridylamino ligands was examined by density functional theory (DFT) and elastic scattering Green’s functions (ESGF) calculations. The calculated results revealed that an intramolecular ferromagnetic (FM) coupling state showed a higher conductivity in comparison with an anti-ferromagnetic (AFM) coupling state. The present results suggest the potential of the complex as a molecular switch as well as a molecular wire. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Graphical abstract

7 pages, 2177 KiB

Open AccessCommunication

A BODIPY-Bridged Bisphenoxyl Diradicaloid: Solvent-Dependent Diradical Character and Physical Properties

by Fang Miao, Hoa Phan and Jishan Wu

Molecules 2019, 24(8), 1446; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24081446 - 12 Apr 2019

Cited by 10 | Viewed by 3832

Abstract

We report a new boron dipyrromethene (BODIPY)-bridged bisphenoxyl diradicaloid (2), which showed closed-shell diamagnetic character in less polar solvents such as dichloromethane but open-shell diradical character with paramagnetic activity in the very polar solvent N,N-dimethylformamide. X-ray crystallographic analysis of 2 revealed an anti-parallel stacked dimer structure via intermolecular dipole–dipole interaction, and the observed solvent-dependent diradical character can be explained by the different dihedral angles between the phenoxyl units and the BODIPY bridge, and structural flexibility of the molecule in different solvents. Compound 2 also exhibited solvent-dependent optical and electrochemical properties. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Figure 1

16 pages, 2515 KiB

Open AccessArticle

Light-Induced Control of the Spin Distribution on Cu–Dithiolene Complexes: A Correlated Ab Initio Study

by Jhon Zapata-Rivera and Carmen J. Calzado

Molecules 2019, 24(6), 1088; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24061088 - 19 Mar 2019

Cited by 3 | Viewed by 2892

Abstract

Metal dithiolene complexes—M(dmit)₂—are key building blocks for magnetic, conducting, and optical molecular materials, with singular electronic structures resulting from the mixing of the metal and dmit ligand orbitals. Their use in the design of magnetic and conducting materials is linked to the control of the unpaired electrons and their localized/delocalized nature. It has been recently found that UV–Vis light can control the spin distribution of some [Cu(dmit)₂]⁻² salts in a direct and reversible way. In this work, we study the optical response of these salts and the origin of the differences observed in the EPR spectra under UV–Vis irradiation by means of wave function-based quantum chemistry methods. The low-lying states of the complex have been characterized and the electronic transitions with a non-negligible oscillator strength have been identified. The population of the corresponding excited states promoted by the UV–Vis absorption produces significant changes in the spin distribution, and could explain the changes observed in the system upon illumination. The interaction between neighbor [Cu(dmit)₂]⁻² complexes is weakly ferromagnetic, consistent with the relative orientation of the magnetic orbitals and the crystal packing, but in disagreement with previous assignments. Our results put in evidence the complex electronic structure of the [Cu(dmit)₂]⁻² radical and the relevance of a multideterminantal approach for an adequate analysis of their properties. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Figure 1

29 pages, 9956 KiB

Open AccessArticle

Linear Response Functions of Densities and Spin Densities for Systematic Modeling of the QM/MM Approach for Mono- and Poly-Nuclear Transition Metal Systems

by Colin K. Kitakawa, Tomohiro Maruyama, Jinta Oonari, Yuki Mitsuta, Takashi Kawakami, Mitsutaka Okumura, Kizashi Yamaguchi and Shusuke Yamanaka

Molecules 2019, 24(4), 821; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24040821 - 25 Feb 2019

Cited by 2 | Viewed by 3319

Abstract

We applied our analysis, based on a linear response function of density and spin density, to two typical transition metal complex systems-the reaction centers of P450, and oxygen evolving center in Photosystem II, both of which contain open-shell transition metal ions. We discuss the relationship between LRF of electron density and spin density and the types of units and interactions of the systems. The computational results are discussed in relation to quantum mechanics (QM) cluster and quantum mechanics/molecular mechanics (QM/MM) modeling that are employed to compute the reaction centers of enzymes. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Figure 1

13 pages, 2398 KiB

Open AccessArticle

A Density Functional Theory-Based Scheme to Compute the Redox Potential of a Transition Metal Complex: Applications to Heme Compound

by Toru Matsui and Jong-Won Song

Molecules 2019, 24(4), 819; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24040819 - 25 Feb 2019

Cited by 3 | Viewed by 4597

Abstract

We estimated the redox potential of a model heme compound by using the combination of our density functionals with a computational scheme, which corrects the solvation energy to the normal solvent model. Among many density functionals, the LC-BOP12 functional gave the smallest mean absolute error of 0.16 V in the test molecular sets. The application of these methods revealed that the redox potential of a model heme can be controlled within 200 mV by changing the protonation state and even within 20 mV by the flipping of the ligand histidine. In addition, the redox potential depends on the inverse of the dielectric constant, which controls the surroundings. The computational results also imply that a system with a low dielectric constant avoids the charged molecule by controlling either the redox potential or the protonation system. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Graphical abstract

15 pages, 360 KiB

Open AccessArticle

by Suryoday Prodhan, Sumit Mazumdar and S. Ramasesha

Molecules 2019, 24(4), 730; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24040730 - 18 Feb 2019

Cited by 7 | Viewed by 2916

Abstract

We report studies of the correlated excited states of coronene and substituted coronene within the Pariser–Parr–Pople (PPP) correlated

π

We report studies of the correlated excited states of coronene and substituted coronene within the Pariser–Parr–Pople (PPP) correlated

π

-electron model employing the symmetry-adapted density matrix renormalization group technique. These polynuclear aromatic hydrocarbons can be considered as graphene nanoflakes. We review their electronic structures utilizing a new symmetry adaptation scheme that exploits electron-hole symmetry, spin-inversion symmetry, and end-to-end interchange symmetry. The study of the electronic structures sheds light on the electron correlation effects in these finite-size graphene analogues, which diminishes going from one-dimensional to higher-dimensional systems, yet is significant within these finite graphene derivatives. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Figure 1

13 pages, 1967 KiB

Open AccessArticle

Monte Carlo Wavefunction Approach to Singlet Fission Dynamics of Molecular Aggregates

by Masayoshi Nakano, Kenji Okada, Takanori Nagami, Takayoshi Tonami, Ryohei Kishi and Yasutaka Kitagawa

Molecules 2019, 24(3), 541; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24030541 - 01 Feb 2019

Cited by 11 | Viewed by 2716

Abstract

We have developed a Monte Carlo wavefunction (MCWF) approach to the singlet fission (SF) dynamics of linear aggregate models composed of monomers with weak diradical character. As an example, the SF dynamics for a pentacene dimer model is investigated by considering the intermolecular electronic coupling and the vibronic coupling. By comparing with the results by the quantum master equation (QME) approach, we clarify the dependences of the MCWF results on the time step (Δt) and the number of MC trajectories (M_C). The SF dynamics by the MCWF approach is found to quantitatively (within an error of 0.02% for SF rate and of 0.005% for double-triplet (TT) yield) reproduce that by the QME approach when using a sufficiently small Δt (~0.03 fs) and a sufficiently large M_C (~10⁵). The computational time (t_req) in the MCWF approach also exhibits dramatic reduction with increasing the size of aggregates (N-mers) as compared to that in the QME approach, e.g., ~34 times faster at the 20-mer, and the size-dependence of t_req shows significant reduction from N^5.15 (QME) to N^3.09 (MCWF). These results demonstrate the promising high performance of the MCWF approach to the SF dynamics in extended multiradical molecular aggregates including a large number of quantum dissipation, e.g., vibronic coupling, modes. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Graphical abstract

22 pages, 5700 KiB

Open AccessArticle

Extent of Spin Contamination Errors in DFT/Plane-wave Calculation of Surfaces: A Case of Au Atom Aggregation on a MgO Surface

by Kohei Tada, Tomohiro Maruyama, Hiroaki Koga, Mitsutaka Okumura and Shingo Tanaka

Molecules 2019, 24(3), 505; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24030505 - 30 Jan 2019

Cited by 26 | Viewed by 3853

Abstract

The aggregation of Au atoms onto a Au dimer (Au₂) on a MgO (001) surface was calculated by restricted (spin-un-polarized) and unrestricted (spin-polarized) density functional theory calculations with a plane-wave basis and the approximate spin projection (AP) method. The unrestricted calculations included spin contamination errors of 0.0–0.1 eV, and the errors were removed using the AP method. The potential energy curves for the aggregation reaction estimated by the restricted and unrestricted calculations were different owing to the estimation of the open-shell structure by the unrestricted calculations. These results show the importance of the open-shell structure and correction of the spin contamination error for the calculation of small-cluster-aggregations and molecule dimerization on surfaces. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Figure 1

14 pages, 2742 KiB

Open AccessArticle

Synthesis, Characterization, Absorption Properties, and Electronic Structures of Paddlewheel-Type Dirhodium(II) Tetra-μ-(n-naphthoate) Complexes: An Experimental and Theoretical Study

by Yusuke Kataoka, Raiki Fukumoto, Natsumi Yano, Daiki Atarashi, Hidekazu Tanaka, Tatsuya Kawamoto and Makoto Handa

Molecules 2019, 24(3), 447; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24030447 - 27 Jan 2019

Cited by 11 | Viewed by 3001

Abstract

The reactions of [Rh₂(O₂CCH₃)₄(OH₂)₂] with n-naphthalenecarboxylic acids (n = 1: 1-HNC, n = 2: 2-HNC) afford the dirhodium tetra-μ-(n-naphthoate) complexes [Rh₂(1-NC)₄] (1) and [Rh₂(2-NC)₄] (2), respectively. Single crystal X-ray diffraction analyses of [1(OCMe₂)₂] and [2(OCMe₂)₂], which were obtained by recrystallization from acetone (OCMe₂) solutions of 1 and 2, reveal that the dirhodium cores are coordinated by four equatorially bridging naphthoate ligands and two axial OCMe₂ ligands. Density functional theory (DFT) calculation confirmed that (i) the single Rh–Rh bond is formed between the two Rh ions and (ii) the electronic structures between two Rh ions in [1(OCMe₂)₂] and [2(OCMe₂)₂] are best described as π⁴δ²σ²δ*²π*⁴ and δ²π⁴σ²δ*²π*⁴, respectively. Time-dependent DFT (TDDFT) calculations clarify the absorption band characters of [1(OCMe₂)₂] and [2(OCMe₂)₂]; the former shows the bands due to d–d and metal–to–metal-ligand charge transfer (MMLCT) excitations in the visible light region, whereas the latter shows the bands due to only d–d excitations in the same region. The electrochemical properties and thermal stabilities of [1(OCMe₂)₂] and [2(OCMe₂)₂] were also investigated in this study. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Graphical abstract

8 pages, 1278 KiB

Open AccessCommunication

Curve Effect on Singlet Diradical Contribution in Kekulé-type Diradicals: A Sensitive Probe for Quinoidal Structure in Curved π-Conjugated Molecules

by Misaki Matsumoto, Ivana Antol and Manabu Abe

Molecules 2019, 24(1), 209; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24010209 - 08 Jan 2019

Cited by 4 | Viewed by 5205

Abstract

Curved (non-planar) aromatic compounds have attracted significant research attention in the fields of basic chemistry and materials science. The contribution of the quinoidal structure in the curved π-conjugated structures has been proposed to be the key for materials functions. In this study, the curve effect on the quinoidal contribution was investigated in Kekulé-type singlet diradicals (S-DR1-4) as a sensitive probe for quinoidal structures in curved π-conjugated molecules. The quinoidal contribution in S-DR1-4 was found to increase with increasing the curvature of the curved structure, which was quantitatively analyzed using NBO analysis and the natural orbital occupation numbers computed by the CASSCF method. The curve effect on the singlet-triplet energy gap was examined by the CASPT2 method. The singlet-triplet energy gaps for the highly π-conjugated diradicals were determined for the first time using the CASPT2 method. Substantial quinoidal contribution was found in the curved structures of the delocalized singlet diradicals S-DR1-4, in contrast to its absence in the corresponding triplet states T-DR1-4. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Graphical abstract

12 pages, 2396 KiB

Open AccessArticle

Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction

by Takaki Tokiwa, Mitsuo Shoji, Vladimir Sladek, Naoki Shibata, Yoshiki Higuchi, Kunishige Kataoka, Takeshi Sakurai, Yasuteru Shigeta and Fuminori Misaizu

Molecules 2019, 24(1), 76; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24010076 - 26 Dec 2018

Cited by 3 | Viewed by 3154

Abstract

Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted density functional theory (UDFT) method was adopted for the open-shell system. We found new candidates of the native intermediate (NI, intermediate II) and the resting oxidized (RO) states, i.e., NI^H+ and RO₀. Elongations of the Cu-Cu atomic distances for the trinuclear Cu center (TNC) and very small structural changes around the type I Cu (T1Cu) were calculated as the results of a four-electron reduction. The QM/MM optimized structures are in good agreement with recent high-resolution X-ray structures. As the structural change in the TNC upon reduction was revealed to be the change in the size of the triangle spanned by the three Cu atoms of TNC, we introduced a new index (l) to characterize the specific structural change. Not only the wild-type, but also the M467Q, which mutates the amino acid residue coordinating T1Cu, were precisely analyzed in terms of their molecular orbital levels, and the optimized redox potential of T1Cu was theoretically reconfirmed. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Graphical abstract

17 pages, 2596 KiB

Open AccessFeature PaperArticle

Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results

by Toru Saito, Manami Fujiwara and Yu Takano

Molecules 2018, 23(12), 3332; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules23123332 - 15 Dec 2018

Cited by 1 | Viewed by 3623

Abstract

We report a reparameterization of PM6 parameters for fluorine and chlorine using our training set containing transition metal complexes. Spin unrestricted calculations with the resulting rPM6 (UrPM6) were examined quantitatively using two test sets: (i) the description of magnetic interactions in 25 dinuclear metal complexes and (ii) the prediction of barrier heights and reaction energies for epoxidation and fluorination reactions catalyzed by high-valent manganese-oxo species. The conventional UPM6 and UPM7 methods were also evaluated for comparison on the basis of either experimental or computational (the UB3LYP/SVP level) outcomes. The merits of UrPM6 are highlighted by both the test sets. As regards magnetic exchange coupling constants, the UrPM6 method had the smallest mean absolute errors from the experimental data (19 cm⁻¹), followed by UPM7 (119 cm⁻¹) and UPM6 (373 cm⁻¹). For the epoxidation and fluorination reactions, all of the transition state searches were successful using UrPM6, while the success rates obtained by UPM6 and UPM7 were only 50%. The UrPM6-optimized stationary points also agreed well with the reference UB3LYP-optimized geometries. The accuracy for estimating reaction energies was also greatly remedied. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Figure 1

Review

Jump to: Research

13 pages, 6127 KiB

Open AccessReview

Synthesis, Physical Properties, and Reactivity of Stable, π-Conjugated, Carbon-Centered Radicals

by Takashi Kubo

Molecules 2019, 24(4), 665; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24040665 - 13 Feb 2019

Cited by 49 | Viewed by 6514

Abstract

Recently, long-lived, organic radical species have attracted much attention from chemists and material scientists because of their unique electronic properties derived from their magnetic spin and singly occupied molecular orbitals. Most stable and persistent organic radicals are heteroatom-centered radicals, whereas carbon-centered radicals are generally very reactive and therefore have had limited applications. Because the physical properties of carbon-centered radicals depend predominantly on the topology of the π-electron array, the development of new carbon-centered radicals is key to new basic molecular skeletons that promise novel and diverse applications of spin materials. This account summarizes our recent studies on the development of novel carbon-centered radicals, including phenalenyl, fluorenyl, and triarylmethyl radicals. Full article

(This article belongs to the Special Issue Open-Shell Systems for Functional Materials)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Open-Shell Systems for Functional Materials

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Published Papers (13 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI