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Advances in Density Functional Theory (DFT) Calculation

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

Deadline for manuscript submissions: 30 June 2024 | Viewed by 14530

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Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok, 50/24, Krasnoyarsk, Russia
Interests: theoretical and experimental investigation of modified natural chemistry compounds; synthesis of new derivatives of natural substances; methods of alkylation and sulfation of polysaccharides and lignin
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Guest Editor
Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, University of Monastir, Monastir, Tunisia
Interests: study of the effect of non-covalent interactions on the structural, vibrational, electronic and biological properties of organic or hybrid compounds; density functional theory; ab-initio calculation; molecular docking

Special Issue Information

Dear Colleagues,

In recent years, various approaches to computing in chemistry, including quantum chemistry, have become increasingly important. This is indicated, firstly, by their constantly expanding application in a large number of diverse areas, such as calculations of various structures and their properties, the development of medicines and new functional materials, etc. Secondly, the active development and general interest in this area science is expressed in the constant growth of the number of publications on the topic of theoretical chemistry, in particular, the theory of the density functional.

The constant development of theoretical chemistry, on the one hand, and the growing needs of experimental chemistry, on the other hand, lead to the development and expansion of the use of density functional theory for calculating various molecular systems and their properties.

The subject of this Special Issue relates to advances in the calculations of various atomic-molecular systems by the density functional theory (DFT) method. This special issue welcomes articles with the results of calculations on new substances, functional materials, solvation models, catalysts and catalytic processes, etc. In addition, articles of a complex nature are also welcome, which present data on experimental and theoretical methods (including QTAIM and etc.) research of materials, the connection between theory and experiment is described. At the same time, review articles both on the Theory of the Density Functional in general and on its application in certain areas and systems, in particular, are also important.

Dr. Aleksandr S. Kazachenko
Dr. Noureddine Issaoui
Guest Editors

Manuscript Submission Information

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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

  • DFT
  • theoretical and computational chemistry
  • new functional materials
  • calculations of new materials and catalysts
  • characterization of the catalytic materials
  • non-covalent interactions (NCI)
  • biological activities
  • electronic proprieties
  • kinetics and catalysis
  • QTAIM

Published Papers (10 papers)

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Research

11 pages, 3408 KiB  
Article
On the Diffusion of Ionic Liquids in ILs@ZIF-8 Composite Materials: A Density Functional Theory Study
by Longlong Liu, Kun Jiang, Qingjun Chen and Lei Liu
Molecules 2024, 29(8), 1697; https://doi.org/10.3390/molecules29081697 - 9 Apr 2024
Viewed by 509
Abstract
Recently, composite materials consisting of ionic liquids (ILs) and metal–organic frameworks (MOFs) have attracted a great deal of attention due to their fantastic properties. Many theoretical studies have been performed on their special structures and gas separation applications. Yet, the mechanism for the [...] Read more.
Recently, composite materials consisting of ionic liquids (ILs) and metal–organic frameworks (MOFs) have attracted a great deal of attention due to their fantastic properties. Many theoretical studies have been performed on their special structures and gas separation applications. Yet, the mechanism for the diffusion of ILs inside MOF channels still remains unclear. Here, the DFT calculations (e.g., rigid and relaxed potential energy surface, PES, scan) together with frontier orbital analysis, natural charge analysis, and energy decomposition analysis were performed to investigate the diffusion behavior of a typical IL, [C4mim][PF6], into the ZIF-8 SOD cage. The PES profiles indicate that it is quite difficult for the cation [C4min]+ to diffuse into the cage of ZIF-8 through the pristine pores because of the large imidazole steric hindrance, which results in a large energy barrier of ca. 40 kcal·mol−1 at the least. Interestingly, the PES reveals that a successful diffusion could be obtained by thermal contributions, which enlarge the pore size through swing effects at higher temperatures. For example, both [C4mim]+ and [PF6] could easily diffuse through the channel of the ZIF-8 SOD cage when the pore size was increased to 6.9 Å. Subsequently, electronic structure analyses reveal that the main interactions between [PF6] or [C4mim]+ and ZIF-8 are the steric repulsion interactions. Finally, the effects of the amounts of [C4mim][PF6] on the ZIF-8 structures were investigated, and the results show that two pairs of [C4mim][PF6] per SOD cage are the most stable in terms of the interaction between energies and structural changes. With these findings, we propose that the high-temperature technique could be employed during the synthesis of IL@MOF membranes, to enrich their family members and their industrial applications. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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17 pages, 2987 KiB  
Article
Marine Toxins as Pharmaceutical Treasure Troves: A Focus on Saxitoxin Derivatives from a Computational Point of View
by Norma Flores-Holguín, Joan S. Salas-Leiva, Erick J. Núñez-Vázquez, Dariel Tovar-Ramírez and Daniel Glossman-Mitnik
Molecules 2024, 29(1), 275; https://doi.org/10.3390/molecules29010275 - 4 Jan 2024
Viewed by 1168
Abstract
This work highlights the significant potential of marine toxins, particularly saxitoxin (STX) and its derivatives, in the exploration of novel pharmaceuticals. These toxins, produced by aquatic microorganisms and collected by bivalve mollusks and other filter-feeding organisms, offer a vast reservoir of chemical and [...] Read more.
This work highlights the significant potential of marine toxins, particularly saxitoxin (STX) and its derivatives, in the exploration of novel pharmaceuticals. These toxins, produced by aquatic microorganisms and collected by bivalve mollusks and other filter-feeding organisms, offer a vast reservoir of chemical and biological diversity. They interact with sodium channels in physiological processes, affecting various functions in organisms. Exposure to these toxins can lead to symptoms ranging from tingling sensations to respiratory failure and cardiovascular shock, with STX being one of the most potent. The structural diversity of STX derivatives, categorized into carbamate, N-sulfocarbamoyl, decarbamoyl, and deoxydecarbamoyl toxins, offers potential for drug development. The research described in this work aimed to computationally characterize 18 STX derivatives, exploring their reactivity properties within marine sponges using conceptual density functional theory (CDFT) techniques. Additionally, their pharmacokinetic properties, bioavailability, and drug-likeness scores were assessed. The outcomes of this research were the chemical reactivity parameters calculated via CDFT as well as the estimated pharmacokinetic and ADME properties derived using computational tools. While they may not align directly, the integration of these distinct datasets enriches our comprehensive understanding of the compound’s properties and potential applications. Thus, this study holds promise for uncovering new pharmaceutical candidates from the considered marine toxins. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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15 pages, 3454 KiB  
Article
Unveiling the Potential of B3O3 Nanoflake as Effective Transporter for the Antiviral Drug Favipiravir: Density Functional Theory Analysis
by Muhammad Nauman Zahid, Naveen Kosar, Hasnain Sajid, Khalid Elfaki Ibrahim, Mansour K. Gatasheh and Tariq Mahmood
Molecules 2023, 28(24), 8092; https://doi.org/10.3390/molecules28248092 - 14 Dec 2023
Cited by 3 | Viewed by 1067
Abstract
In this study, for the first time, boron oxide nanoflake is analyzed as drug carrier for favipiravir using computational studies. The thermodynamic stability of the boron oxide and favipiravir justifies the strong interaction between both species. Four orientations are investigated for the interaction [...] Read more.
In this study, for the first time, boron oxide nanoflake is analyzed as drug carrier for favipiravir using computational studies. The thermodynamic stability of the boron oxide and favipiravir justifies the strong interaction between both species. Four orientations are investigated for the interaction between the favipiravir and the B3O3 nanoflake. The Eint of the most stable orientation is −26.98 kcal/mol, whereas the counterpoise-corrected energy is −22.59 kcal/mol. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) analyses are performed to obtain insights about the behavior and the types of interactions that occur between B3O3 nanoflake and favipiravir. The results indicate the presence of hydrogen bonding between the hydrogen in the favipiravir and the oxygen in the B3O3 nanoflake in the most stable complex (FAV@B3O3-C1). The electronic properties are investigated through frontier molecular orbital analysis, dipole moments and chemical reactivity descriptors. These parameters showed the significant activity of B3O3 for favipiravir. NBO charge analysis transfer illustrated the charge transfer between the two species, and UV-VIS analysis confirmed the electronic excitation. Our work suggested a suitable drug carrier system for the antiviral drug favipiravir, which can be considered by the experimentalist for better drug delivery systems. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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21 pages, 3715 KiB  
Article
Density Functional Theory and Density Functional Tight Binding Studies of Thiamine Hydrochloride Hydrates
by Ewa Napiórkowska, Łukasz Szeleszczuk, Katarzyna Milcarz and Dariusz Maciej Pisklak
Molecules 2023, 28(22), 7497; https://doi.org/10.3390/molecules28227497 - 9 Nov 2023
Viewed by 1134
Abstract
Thiamine hydrochloride (THCL), also known as vitamin B1, is an active pharmaceutical ingredient (API), present on the list of essential medicines developed by the WHO, which proves its importance for public health. THCL is highly hygroscopic and can occur in the [...] Read more.
Thiamine hydrochloride (THCL), also known as vitamin B1, is an active pharmaceutical ingredient (API), present on the list of essential medicines developed by the WHO, which proves its importance for public health. THCL is highly hygroscopic and can occur in the form of hydrates with varying degrees of hydration, depending on the air humidity. Although experimental characterization of the THCL hydrates has been described in the literature, the questions raised in previously published works suggest that additional research and in-depth analysis of THCL dehydration behavior are still needed. Therefore, the main aim of this study was to characterize, by means of quantum chemical calculations, the behavior of thiamine hydrates and explain the previously obtained results, including changes in the NMR spectra, at the molecular level. To achieve this goal, a series of DFT (CASTEP) and DFTB (DFTB+) calculations under periodic boundary conditions have been performed, including molecular dynamics simulations and GIPAW NMR calculations. The obtained results explain the differences in the relative stability of the studied forms and changes in the spectra observed for the samples of various degrees of hydration. This work highlights the application of periodic DFT calculations in the analysis of various solid forms of APIs. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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7 pages, 1497 KiB  
Communication
Theoretical Prediction of the Anti-Icing Activity of Two-Dimensional Ice I
by Sicheng Liu, Xiaoyan Liu, Yining Li, Qing Guo, Xiangting Yu, Yi Yin, Haoze Jing and Peng Zhang
Molecules 2023, 28(16), 6145; https://doi.org/10.3390/molecules28166145 - 20 Aug 2023
Viewed by 897
Abstract
Two-dimensional (2D) ice I is atomic-level ice that is composed of two interlocked atomic layers saturated with hydrogen bonds. It has recently been experimentally observed, but its properties have yet to be clarified. Accordingly, we theoretically studied the hydrophobic properties of 2D ice [...] Read more.
Two-dimensional (2D) ice I is atomic-level ice that is composed of two interlocked atomic layers saturated with hydrogen bonds. It has recently been experimentally observed, but its properties have yet to be clarified. Accordingly, we theoretically studied the hydrophobic properties of 2D ice I. On the contrary, a simulation of a hydrogen fluoride molecule on a 2D ice surface manifested that it destroyed the 2D ice structure and connected new hydrogen bonds with water molecules. Investigations of the interfacial effect between 2D and three-dimensional (3D) ice films indicated that the network structure of 2D ice was not destroyed by a 3D ice surface, as the former was saturated with hydrogen bonds. However, the surface of 3D ice reorganized to form as many hydrogen bonds as possible. Thus, the 2D ice film was hydrophobic and inhibited the growth of 3D ice. This shows that if 2D ice can be produced on an industrial scale, it can be used as an anti-3D-icing agent under low temperatures. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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13 pages, 5409 KiB  
Article
Density Functional Theory Study of CO2 Hydrogenation on Transition-Metal-Doped Cu(211) Surfaces
by Yushan Wang, Mengting Yu, Xinyi Zhang, Yujie Gao, Jia Liu, Ximing Zhang, Chunxiao Gong, Xiaoyong Cao, Zhaoyang Ju and Yongwu Peng
Molecules 2023, 28(6), 2852; https://doi.org/10.3390/molecules28062852 - 22 Mar 2023
Cited by 1 | Viewed by 1906
Abstract
The massive emission of CO2 has caused a series of environmental problems, including global warming, which exacerbates natural disasters and human health. Cu-based catalysts have shown great activity in the reduction of CO2, but the mechanism of CO2 activation [...] Read more.
The massive emission of CO2 has caused a series of environmental problems, including global warming, which exacerbates natural disasters and human health. Cu-based catalysts have shown great activity in the reduction of CO2, but the mechanism of CO2 activation remains ambiguous. In this work, we performed density functional theory (DFT) calculations to investigate the hydrogenation of CO2 on Cu(211)-Rh, Cu(211)-Ni, Cu(211)-Co, and Cu(211)-Ru surfaces. The doping of Rh, Ni, Co, and Ru was found to enhance CO2 hydrogenation to produce COOH. For CO2 hydrogenation to produce HCOO, Ru plays a positive role in promoting CO dissociation, while Rh, Ni, and Co increase the barriers. These results indicate that Ru is the most effective additive for CO2 reduction in Cu-based catalysts. In addition, the doping of Rh, Ni, Co, and Ru alters the electronic properties of Cu, and the activity of Cu-based catalysts was subsequently affected according to differential charge analysis. The analysis of Bader charge shows good predictions for CO2 reduction over Cu-based catalysts. This study provides some fundamental aids for the rational design of efficient and stable CO2-reducing agents to mitigate CO2 emission. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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17 pages, 4634 KiB  
Article
Synthesis, Empirical and Theoretical Investigations on New Histaminium Bis(Trioxonitrate) Compound
by Mahdi Jmai, Sofian Gatfaoui, Noureddine Issaoui, Thierry Roisnel, Aleksandr S. Kazachenko, Omar Al-Dossary, Houda Marouani and Anna S. Kazachenko
Molecules 2023, 28(4), 1931; https://doi.org/10.3390/molecules28041931 - 17 Feb 2023
Cited by 5 | Viewed by 1622
Abstract
In this paper, a novel hybrid material, entitled histaminium bis(trioxonitrate), with the general chemical formula (C5H11N3)(NO3)2, denoted by HTN was presented. Single-crystal X-ray diffraction was used to determine the structural characteristics of this [...] Read more.
In this paper, a novel hybrid material, entitled histaminium bis(trioxonitrate), with the general chemical formula (C5H11N3)(NO3)2, denoted by HTN was presented. Single-crystal X-ray diffraction was used to determine the structural characteristics of this compound after it was made using a slow evaporation method at room temperature. This compound was elaborated and crystallized to the monoclinic system with space group P21/c, and the lattice parameters obtained were: a = 10.4807 (16)Å, b = 11.8747 (15)Å, c = 16.194 (2)Å, β = 95.095 (6)°, V = 2007.4 (5)Å3 and Z = 8. The title compound’s atomic structure couldbe modeled as a three-dimensional network. Organic cations and nitrate anions were connected via N–H...O and C–H...O hydrogen bonds in the HTN structure. The intermolecular interactions responsible for the formation of crystal packing were evaluated using Hirshfeld surfaces and two-dimensional fingerprint plots. The compound’s infrared spectrum, which ranged from 4000 to 400 cm−1, confirmed the presence of the principal bands attributed to the internal modes of the organic cation and nitrate anions. Additionally, spectrofluorimetry and the ultraviolet–visible spectrum was used to investigate this compound. DFT calculations were used to evaluate the composition and properties of HTN. The energy gap, chemical reactivity and crystal stability of HTN were quantified by performing HOMO-LUMO frontier orbitals analysis. Topological analysis (AIM), Reduced Density Gradient (RDG), molecular electrostatic potential surface (MEPS) and Mulliken population were processed to determine the types of non-covalent interactions, atomic charges and molecular polarity in detail. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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12 pages, 4975 KiB  
Article
Investigation on Gold–Ligand Interaction for Complexes from Gold Leaching: A DFT Study
by Na Zhang, Jue Kou and Chunbao Sun
Molecules 2023, 28(3), 1508; https://doi.org/10.3390/molecules28031508 - 3 Feb 2023
Cited by 4 | Viewed by 1863
Abstract
Gold leaching is an important process to extract gold from ore. Conventional alkaline cyanide process and alternative nontoxic lixiviants including thiosulfate, thiourea, thiocyanate, and halogen have been widely investigated. However, density functional theory (DFT) study on the gold complexes Au(CN)2, [...] Read more.
Gold leaching is an important process to extract gold from ore. Conventional alkaline cyanide process and alternative nontoxic lixiviants including thiosulfate, thiourea, thiocyanate, and halogen have been widely investigated. However, density functional theory (DFT) study on the gold complexes Au(CN)2, Au(S2O3)23−, Au[SC(NH2)2]2+, Au(SCN)2, and AuCl2 required for discovering and designing new highly efficient and environmentally friendly gold leaching reagents is lacking, which is expected to support constructive information for the discovery and designation of new high-efficiency and environmentally friendly gold leaching reagents. In this study, the structure information, electron-transferring properties, orbital interaction, and chemical bond composition for complexes Au(CN)2, Au(S2O3)23−, Au[SC(NH2)2]2+, Au(SCN)2, and AuCl2 depending on charge decomposition analysis (CDA), natural bond orbital (NBO), natural resonance theory (NRT), electron localization function (ELF), and energy decomposition analysis (EDA) were performed based on DFT calculation. The results indicate that there is not only σ-donation from ligand to Au+, but also electron backdonation from Au+ to ligands, which strengthens the coordinate bond between them. Compared with Cl, ligands CN, S2O32−, SC(NH2)2, and SCN have very large covalent contribution to the coordinate bond with Au+, which explains the special stability of Au-CN and Au-S bonds. The degree of covalency and bond energy in Au–ligand bonding decreases from Au(CN)2, Au(S2O3)23−, Au[SC(NH2)2]2+, Au(SCN)2, to AuCl2, which interprets the stability of the five complexes: Au(CN)2 > Au(S2O3)23− > Au[SC(NH2)2]2+ > Au(SCN)2 > AuCl2. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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33 pages, 17337 KiB  
Article
Comprehensive Study of the Ammonium Sulfamate–Urea Binary System
by Aleksandr S. Kazachenko, Noureddine Issaoui, Olga Yu. Fetisova, Yaroslava D. Berezhnaya, Omar M. Al-Dossary, Feride Akman, Naveen Kumar, Leda G. Bousiakou, Anna S. Kazachenko, Vladislav A. Ionin, Evgeniy V. Elsuf’ev and Angelina V. Miroshnikova
Molecules 2023, 28(2), 470; https://doi.org/10.3390/molecules28020470 - 4 Jan 2023
Cited by 2 | Viewed by 1562
Abstract
The physicochemical properties of binary systems are of great importance for the application of the latter. We report on the investigation of an ammonium sulfamate–urea binary system with different component ratios using a combination of experimental (FTIR, XRD, TGA/DSC, and melting point) and [...] Read more.
The physicochemical properties of binary systems are of great importance for the application of the latter. We report on the investigation of an ammonium sulfamate–urea binary system with different component ratios using a combination of experimental (FTIR, XRD, TGA/DSC, and melting point) and theoretical (DFT, QTAIM, ELF, RDG, ADMP, etc.) techniques. It is shown that, at a temperature of 100 °C, the system under study remains thermally and chemically stable for up to 30 min. It was established using X-ray diffraction analysis that the heating time barely affects the X-ray characteristics of the system. Data on the aggregate states in specified temperature ranges were obtained with thermal analysis and determination of the melting point. The structures of the ammonium sulfamate–urea system with different component ratios were optimized within the density functional theory. The atom-centered density matrix propagation calculation of the ammonium sulfamate–urea system with different component ratios was performed at temperatures of 100, 300, and 500 K. Regardless of the component ratio, a regular increase in the potential energy variation (curve amplitude) with an increase in temperature from 100 to 500 K was found. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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19 pages, 4460 KiB  
Article
A Comprehensive Study of N-Butyl-1H-Benzimidazole
by Aleksandr S. Kazachenko, Emine Tanış, Feride Akman, Mouna Medimagh, Noureddine Issaoui, Omar Al-Dossary, Leda G. Bousiakou, Anna S. Kazachenko, Dmitry Zimonin and Andrey M. Skripnikov
Molecules 2022, 27(22), 7864; https://doi.org/10.3390/molecules27227864 - 14 Nov 2022
Cited by 4 | Viewed by 1683
Abstract
Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl [...] Read more.
Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl substituent in the N position does not significantly affect the conjugation and structural organization of benzimidazole. The optimized molecular parameters were performed by the DFT/B3LYP method with 6-311++G(d,p) basis set. This level of theory shows excellent concurrence with the experimental data. The non-covalent interactions that existed within our compound N-Butyl-1H-benzimidazole were also analyzed by the AIM, RDG, ELF, and LOL topological methods. The color shades of the ELF and LOL maps confirm the presence of bonding and non-bonding electrons in N-Butyl-1H-benzimidazole. From DFT calculations, various methods such as molecular electrostatic potential (MEP), Fukui functions, Mulliken atomic charges, and frontier molecular orbital (HOMO-LUMO) were characterized. Furthermore, UV-Vis absorption and natural bond orbital (NBO) analysis were calculated. It is shown that the experimental and theoretical spectra of N-Butyl-1H-benzimidazole have a peak at 248 nm; in addition, the experimental spectrum has a peak near 295 nm. The NBO method shows that the delocalization of the aσ-electron from σ (C1–C2) is distributed into antibonding σ* (C1–C6), σ* (C1–N26), and σ* (C6–H11), which leads to stabilization energies of 4.63, 0.86, and 2.42 KJ/mol, respectively. Spectroscopic investigations of N-Butyl-1H-benzimidazole were carried out experimentally and theoretically to find FTIR vibrational spectra. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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