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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 20197

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Dr. Aleksandr S. Kazachenko

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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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Dr. Noureddine Issaoui

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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

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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

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Research

11 pages, 3408 KiB

Open AccessArticle

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

Cited by 1 | Viewed by 961

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 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

Open AccessArticle

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

Cited by 1 | Viewed by 2080

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 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

Open AccessArticle

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 8 | Viewed by 1481

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 between the favipiravir and the B₃O₃ nanoflake. The E_int 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

Open AccessArticle

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

Cited by 1 | Viewed by 1697

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 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

Open AccessCommunication

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 1152

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 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

Open AccessArticle

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 2 | Viewed by 2524

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 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

Open AccessArticle

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 6 | Viewed by 2050

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 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

Open AccessArticle

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 5 | Viewed by 2504

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⁻, 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

Open AccessArticle

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 2052

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 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

Open AccessArticle

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 6 | Viewed by 2159

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 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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