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Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes
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Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes

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 (15 October 2020) | Viewed by 18795

Special Issue Editor

Prof. Dr. Oleg V. Mikhailov

E-Mail Website
Guest Editor
Department of Analytical Chemistry, National Research Technological University, K. Marx Street 68, 420015 Kazan, Russia
Interests: coordination chemistry; quantum chemistry; chemistry of macrocyclic compounds; nanosciences; scientometrics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the last 20–25 years, metal complexes formed by chelating and macrocyclic organic and organo-element ligands (in particular, various crown ethers, cryptands, calixarenes, and porphyrins) have gained particular interest in coordination and inorganic chemistry. These compounds have a number of specific (sometimes unique) properties, due to which they have found many applications in various fields of science and in the practice of anthropogenic activities. In connection with this, it is important to predict their physicochemical parameters that determine these very properties, a problem that is currently being successfully solved thanks to the availability of modern quantum-chemical methods of calculation [and above all the density functional theory (DFT) method], as well as computer technologies and related experimental equipment. At the same time, in the literature there have been relatively few theoretical works devoted to quantum-chemical calculations of the above-mentioned metal complexes using the DFT method and more advanced methods.

Original full articles and short communications devoted to quantum-chemical calculations of metal complexes of p-, d-, and f-elements, with open and closed circuits formed by organic and organo-element ligands, are preferred for this Special Issue. We welcome articles in which, along with the required quantum-chemical calculations, experimental data is presented to evaluate the reliability of these calculations. Review articles may also be submitted for publication (including author reviews, the emphasis of which is mainly on the authors’ work).

Prof. Dr. Oleg V. Mikhailov
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Published Papers (7 papers)

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Editorial

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3 pages, 149 KiB  
Editorial
Preface from the Guest Editor of Special Issue “Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes”
by Oleg V. Mikhailov
Int. J. Mol. Sci. 2020, 21(7), 2339; https://doi.org/10.3390/ijms21072339 - 28 Mar 2020
Cited by 1 | Viewed by 1357
Abstract
As is known, in the last fifty years of coordination of inorganic and organo-elemental chemistry, chemical compounds formed by chelating or macrocyclic organic and organo-elemental ligands (in particular, crown ethers, cryptands, calixarenes, cucurbituryls, porphyrins, and their various derivatives) and ions of various p [...] Read more.
As is known, in the last fifty years of coordination of inorganic and organo-elemental chemistry, chemical compounds formed by chelating or macrocyclic organic and organo-elemental ligands (in particular, crown ethers, cryptands, calixarenes, cucurbituryls, porphyrins, and their various derivatives) and ions of various p-, d- and f-elements, have become of special interest [...] Full article
(This article belongs to the Special Issue Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes)

Research

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13 pages, 2373 KiB  
Article
DFT Quantum-Chemical Modeling Molecular Structures of Cobalt Macrocyclic Complexes with Porphyrazine or Its Benzo-Derivatives and Two Oxygen Acido Ligands
by Oleg V. Mikhailov and Denis V. Chachkov
Int. J. Mol. Sci. 2020, 21(23), 9085; https://doi.org/10.3390/ijms21239085 - 29 Nov 2020
Cited by 13 | Viewed by 2488
Abstract
Based on the results of a quantum chemical calculation using the DFT method with the OPBE/TZVP and B3PW91/TZVP levels, the possibility of the existence of three cobalt heteroligand complexes containing in the inner coordination sphere porphyrazine, di[benzo]- and tetra[benzo]porphyrazine, and two oxygen (O [...] Read more.
Based on the results of a quantum chemical calculation using the DFT method with the OPBE/TZVP and B3PW91/TZVP levels, the possibility of the existence of three cobalt heteroligand complexes containing in the inner coordination sphere porphyrazine, di[benzo]- and tetra[benzo]porphyrazine, and two oxygen (O2−) ions with probable oxidation state VI of Co, which is unknown for this element at the present time, was shown. Data on the structural parameters are presented. It was shown that CoN4 chelate nodes as well as all metal-chelate and non-chelate cycles in each of these complexes, were strictly planar. Besides, the bond angles formed by two donor nitrogen atoms and a Co atom were close or equal to 90°, while the bond angles formed by donor atoms N, Co, and O, in most cases, albeit insignificantly, differed from this value. Good agreement between the calculated data obtained using the above two versions of the DFT method was found. Standard thermodynamic parameters of formation (standard enthalpy ΔH0f, 298, entropy S0f, 298 and Gibbs’s energy ΔG0f, 298) for the indicated complexes were presented too. Full article
(This article belongs to the Special Issue Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes)
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20 pages, 7450 KiB  
Article
Evaluating the Performance of a Non-Bonded Cu2+ Model Including Jahn−Teller Effect into the Binding of Tyrosinase Inhibitors
by Lucas Sousa Martins, Jerônimo Lameira, Hendrik G. Kruger, Cláudio Nahum Alves and José Rogério A. Silva
Int. J. Mol. Sci. 2020, 21(13), 4783; https://doi.org/10.3390/ijms21134783 - 06 Jul 2020
Cited by 14 | Viewed by 3189
Abstract
Tyrosinase (TYR) is a metalloenzyme classified as a type-3 copper protein, which is involved in the synthesis of melanin through a catalytic process beginning with the conversion of the amino acid l-Tyrosine (l-Tyr) to l-3,4-dihydroxyphenylalanine (l-DOPA). It [...] Read more.
Tyrosinase (TYR) is a metalloenzyme classified as a type-3 copper protein, which is involved in the synthesis of melanin through a catalytic process beginning with the conversion of the amino acid l-Tyrosine (l-Tyr) to l-3,4-dihydroxyphenylalanine (l-DOPA). It plays an important role in the mechanism of melanogenesis in various organisms including mammals, plants, and fungi. Herein, we used a combination of computational molecular modeling techniques including molecular dynamic (MD) simulations and the linear interaction energy (LIE) model to evaluate the binding free energy of a set of analogs of kojic acid (KA) in complex with TYR. For the MD simulations, we used a dummy model including the description of the Jahn–Teller effect for Cu2+ ions in the active site of this enzyme. Our results show that the LIE model predicts the TYR binding affinities of the inhibitor in close agreement to experimental results. Overall, we demonstrate that the classical model provides a suitable description of the main interactions between analogs of KA and Cu2+ ions in the active site of TYR. Full article
(This article belongs to the Special Issue Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes)
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12 pages, 2660 KiB  
Article
DFT Study of Molecular and Electronic Structure of Ca(II) and Zn(II) Complexes with Porphyrazine and tetrakis(1,2,5-thiadiazole)porphyrazine
by Arseniy A. Otlyotov, Igor V. Ryzhov, Ilya A. Kuzmin, Yuriy A. Zhabanov, Maxim S. Mikhailov and Pavel A. Stuzhin
Int. J. Mol. Sci. 2020, 21(8), 2923; https://doi.org/10.3390/ijms21082923 - 22 Apr 2020
Cited by 14 | Viewed by 2023
Abstract
Electronic and geometric structures of Ca(II) and Zn(II) complexes with porphyrazine (Pz) and tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) were investigated by density functional theory (DFT) calculations and compared. The perimeter of the coordination cavity was found to be practically independent on the nature of a metal [...] Read more.
Electronic and geometric structures of Ca(II) and Zn(II) complexes with porphyrazine (Pz) and tetrakis(1,2,5-thiadiazole)porphyrazine (TTDPz) were investigated by density functional theory (DFT) calculations and compared. The perimeter of the coordination cavity was found to be practically independent on the nature of a metal and a ligand. According to the results of the natural bond orbital (NBO) analysis and quantum theory of atoms in molecules (QTAIM) calculations, Ca–N bonds possess larger ionic contributions as compared to Zn–N. The model electronic absorption spectra obtained with the use of time-dependent density functional theory (TDDFT) calculations indicate a strong bathochromic shift (~70 nm) of the Q-band with a change of Pz ligand by TTDPz for both Ca and Zn complexes. Additionally, CaTTDPz was synthesized and its electronic absorption spectrum was recorded in pyridine and acetone. Full article
(This article belongs to the Special Issue Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes)
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8 pages, 1057 KiB  
Article
Prediction of Binding Stability of Pu(IV) and PuO2(VI) by Nitrogen Tridentate Ligands in Aqueous Solution
by Keunhong Jeong, Hye Jin Jeong, Seung Min Woo and Sungchul Bae
Int. J. Mol. Sci. 2020, 21(8), 2791; https://doi.org/10.3390/ijms21082791 - 17 Apr 2020
Cited by 5 | Viewed by 2283
Abstract
Plutonium has potential applications in energy production in well-controlled nuclear reactors. Since nuclear power plants have great merit as environmentally friendly energy sources with a recyclable system, a recycling system for extracting Pu from spent fuels using suitable extractants has been proposed. Pu [...] Read more.
Plutonium has potential applications in energy production in well-controlled nuclear reactors. Since nuclear power plants have great merit as environmentally friendly energy sources with a recyclable system, a recycling system for extracting Pu from spent fuels using suitable extractants has been proposed. Pu leakage is a potential environmental hazard, hence the need for chemical sensor development. Both extractants and chemical sensors involve metal–ligand interactions and to develop efficient extractants and chemical sensors, structural information about Pu ligands must be obtained by quantum calculations. Herein, six representative nitrogen tridentate ligands were introduced, and their binding stabilities were evaluated. The tridentate L6, which contains tri-pyridine chelate with benzene connectors, showed the highest binding energies for Pu(IV) and PuO2(VI) in water. Analysis based on the quantum theory of atoms in molecular analysis, including natural population analysis and electron density studies, provided insight into the bonding characteristics for each structure. We propose that differences in ionic bonding characteristics account for the Pu-ligand stability differences. These results form a basis for designing novel extractants and organic Pu sensors. Full article
(This article belongs to the Special Issue Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes)
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9 pages, 1209 KiB  
Article
M(VI) Oxidation State Stabilization in Iron, Cobalt and Nickel Heteroligand Metal Chelates Containing 3,7,11,15-Tetraazaporphine and Two Axial Oxo Ligands: Quantum-Chemical Simulation
by Oleg V. Mikhailov and Denis V. Chachkov
Int. J. Mol. Sci. 2020, 21(4), 1494; https://doi.org/10.3390/ijms21041494 - 22 Feb 2020
Cited by 9 | Viewed by 2620
Abstract
The quantum-chemical calculation of iron, cobalt and nickel heteroligand complexes with the double deprotonated form of (NNNN)-donor atomic ligand—3,7,11,15-tetraazaporphine—and two oxo ligands has been carried out. Data on the structural and standard thermodynamic parameters, NBO analysis and multiplicity of the ground states of [...] Read more.
The quantum-chemical calculation of iron, cobalt and nickel heteroligand complexes with the double deprotonated form of (NNNN)-donor atomic ligand—3,7,11,15-tetraazaporphine—and two oxo ligands has been carried out. Data on the structural and standard thermodynamic parameters, NBO analysis and multiplicity of the ground states of these complexes have been presented. The given calculation has been made by using the density functional theory (DFT) method with the OPBE/TZVP basis set. Based on the results of this calculation, the possibility of the existence of oxidation state VI for the chemical elements indicated above—unusual for iron and cobalt, and for nickel, unknown at all—has been shown. Full article
(This article belongs to the Special Issue Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes)
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18 pages, 6097 KiB  
Article
Degradation of Human Serum Albumin by Infrared Free Electron Laser Enhanced by Inclusion of a Salen-Type Schiff Base Zn (II) Complex
by Yuika Onami, Takayasu Kawasaki, Hiroki Aizawa, Tomoyuki Haraguchi, Takashiro Akitsu, Koichi Tsukiyama and Mauricio A. Palafox
Int. J. Mol. Sci. 2020, 21(3), 874; https://doi.org/10.3390/ijms21030874 - 29 Jan 2020
Cited by 11 | Viewed by 4195
Abstract
A salen-type Schiff base Zn(II) complex included in human serum albumin (HSA) protein was examined by UV-Vis, circular dichroism (CD), and fluorescence (PL) spectra. The formation of the composite material was also estimated by a GOLD program of ligand–protein docking simulation. A composite [...] Read more.
A salen-type Schiff base Zn(II) complex included in human serum albumin (HSA) protein was examined by UV-Vis, circular dichroism (CD), and fluorescence (PL) spectra. The formation of the composite material was also estimated by a GOLD program of ligand–protein docking simulation. A composite cast film of HSA and Zn(II) complex was prepared, and the effects of the docking of the metal complex on the degradation of protein molecules by mid-infrared free electron laser (IR-FEL) were investigated. The optimum wavelengths of IR-FEL irradiation to be used were based on experimental FT-IR spectra and vibrational analysis. Using TD-DFT results with 6-31G(d,p) and B3LYP, the IR spectrum of Zn(II) complex could be reasonably assigned. The respective wavelengths were 1652 cm−1 (HSA amide I), 1537 cm−1 (HSA amide II), and 1622 cm−1 (Zn(II) complex C=N). Degradation of HSA based on FT-IR microscope (IRM) analysis and protein secondary structure analysis program (IR-SSE) revealed that the composite material was degraded more than pure HSA or Zn(II) complex; the inclusion of Zn(II) complex enhanced destabilization of folding of HSA. Full article
(This article belongs to the Special Issue Quantum-Chemical Modeling and Design of Chelate and Macrocyclic Metal Complexes)
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