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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: closed (30 April 2024) | Viewed by 15421

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Special Issue Editors

Dr. Muhammad Khalid

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Guest Editor

Department of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
Interests: density functional theory; photovoltaic properties; structural modifications; organic solar cells; NLO materials; electronic structure calculations; modelling of optoelectronic materials; chemosensors
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Dr. Muhammad Nadeem Arshad

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Department of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
Interests: polymer; organic photovolatic polymers; electronic structure calculations; modelling of optoelectronic materials; non-fullerene polymers; Density Functional Theory (DFT)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Density functional theory (DFT) has shown unsurpassed influence in computational chemistry in terms of its performance, compared to wave-function-based electron correlation methods. DFT constitutes an outset for dynamical mean field theory, many-body perturbation theory, density functional perturbation theory, and so forth. Through quantum mechanics, DFT has enabled researchers to evaluate characteristics of molecules, bulk crystals, biological matter and nanodevices. Consequently, DFT has risen to prominence in computational, as well as theoretical, chemistry. However, narrow computational intricacy leads to limited DFT applications. Hence, developing new accelerating computational algorithms to obtain coherent results for complex systems at a feasible computational price is imperative. Linear scaling techniques describe an array of such strategies where the cost of computation corresponds to the size of the structure. At present, technical and fundamental research surrounds excitations in solids and molecules by employing theoretical methods. Further, DFT-based analysis has been one of the most basic and important strategies for drug discovery, allowing the prediction of molecular interactions that hold together a protein and a ligand in the bound state.

The present Special Issue aims to examine new techniques such as combining computational chemistry and machine learning methods, mechanistic study, chemosensor behavior, photovoltaic and opto-electronic properties (NLO and solar cells), to obtain insightful information from DFT methods that are applicable to molecules. We welcome research articles beyond the traditional areas of DFT study, such as applying machine learning to the design and analysis of new materials.

Dr. Muhammad Khalid
Dr. Muhammad Nadeem Arshad
Guest Editors

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Keywords

density functional theory
electronic structure calculations
structural modifications
drug discovery study
modelling of optoelectronic materials
photovoltaic properties
organic solar cells
NLO materials
machine learning
chemosensor exploration

Published Papers (9 papers)

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Research

17 pages, 19240 KiB

Open AccessArticle

Influence of the Tensile Strain on Electron Transport of Ultra-Thin SiC Nanowires

by Qin Tan, Jie Li, Kun Liu, Rukai Liu and Vladimir Skuratov

Molecules 2024, 29(3), 723; https://doi.org/10.3390/molecules29030723 - 04 Feb 2024

Viewed by 627

Abstract

The influence of nanomechanical tensile behavior on electron transport is especially interesting for ultra-thin SiC nanowires (NWs) with different diameters. Our studies theoretically show that these NWs can hold stable electron transmission in some strain ranges and that stretching can enhance the electron transmission around the Fermi level (E_F) at the strains over 0.5 without fracture for a single-atom SiC chain and at the strains not over 0.5 for thicker SiC NWs. For each size of SiC NW, the tensile strain has a tiny effect on the number of device density of states (DDOSs) peaks but can increase the values. Freshly broken SiC NWs also show certain values of DDOSs around E_F. The maximum DDOS increases significantly with the diameter, but interestingly, the DDOS at E_F shows little difference among the three sizes of devices in the late stage of the stretching. Essentially, high electron transmission is influenced by high DDOSs and delocalized electronic states. Analysis of electron localization functions (ELFs) indicates that appropriate tensile stress can promote continuous electronic distributions to contribute electron transport, while excessively large stretching deformation of SiC NWs would split electronic distributions and consequently hinder the movement of electrons. These results provide strong theoretical support for the use of ultra-thin SiC NWs in nano-sensors for functional and controllable electronic devices. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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13 pages, 8859 KiB

Open AccessArticle

Effect of Vacancy, As, and Sb Dopants on the Gold-Capturing Ability of Cu₂S during Gold Collection in Matte Processes

by Hui Huang, Huihui Xiong and Lei Gan

Molecules 2023, 28(21), 7390; https://doi.org/10.3390/molecules28217390 - 02 Nov 2023

Viewed by 585

Abstract

The technique of gold collection in matte can effectively improve the trapping efficiency of precious metals such as gold, silver, and platinum. However, the underlying mechanism of gold collection from high-temperature molten matte is complex and not well understood. In this work, the first-principle calculations were utilized to investigate the adsorption behavior of gold atoms on a Cu₂S surface. The effects of vacancies and As and Sb doping on the gold-trapping ability of Cu₂S were also explored, and the electronic properties of each adsorption system, including the charge density difference, density of states, and charge transfer, were systematically analyzed. The results show that the Cu-terminated Cu₂S(111) surface has the lowest surface energy, and the Au atom is chemically adsorbed on the Cu₂S(111) with an adsorption energy of −1.99 eV. The large adsorption strength is primarily ascribed to the strong hybridizations between Au-5d and Cu-3d orbitals. Additionally, the Cu vacancy can significantly weaken the adsorption strength of Cu₂S(111) towards Au atoms, while the S vacancy can notably enhance it. Moreover, due to the formation of strong covalent As–Au/Sb–Au bonds, doping As and Sb into Cu₂S(111) can enhance the gold-trapping capability of Cu₂S, and the Sb doping exhibits superior effectiveness. Our studied results can provide theoretical guidance for improving the gold collection efficiency of Cu₂S. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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17 pages, 7111 KiB

Open AccessArticle

Exploring the Mechanism of the Intramolecular Diels–Alder Reaction of (2E,4Z,6Z)-2(allyloxy)cycloocta-2,4,6-trien-1-one Using Bonding Evolution Theory

by Abel Idrice Adjieufack, Jean Moto Ongagna, Jean Serge Essomba, Monique Bassomo Ewonkem, Mónica Oliva, Vicent Sixte Safont and Juan Andrés

Molecules 2023, 28(19), 6755; https://doi.org/10.3390/molecules28196755 - 22 Sep 2023

Viewed by 700

Abstract

In the present work, the bond breaking/forming events along the intramolecular Diels–Alder (IMDA) reaction of (2E,4Z,6Z)-2(allyloxy)cycloocta-2,4,6-trien-1-one have been revealed within bonding evolution theory (BET) at the density functional theory level, using the M05-2X functional with the cc-pVTZ basis set. Prior to achieving this task, the energy profiles and stationary points at the potential energy surface (PES) have been characterized. The analysis of the results finds that this rearrangement can proceed along three alternative reaction pathways (a–c). Paths a and b involve two steps, while path c is a one-step process. The first step in path b is kinetically favored, and leads to the formation of an intermediate step, Int-b. Further evolution from Int-b leads mainly to 3-b1. However, 2 is the thermodynamically preferred product and is obtained at high temperatures, in agreement with the experimental observations. Regarding the BET analysis along path b, the breaking/forming process is described by four structural stability domains (SSDs) during the first step, which can be summarized as follows: (1) the breaking of the C–O bond with the transfer of its population to the lone pair (V(O)), (2) the reorganization of the electron density with the creation of two V(C) basins, and (3) the formation of a new C–C single bond via the merger of the two previous V(C) basins. Finally, the conversion of Int-b (via TS2-b1) occurs via the reorganization of the electron density during the first stage (the creation of different pseudoradical centers on the carbon atoms as a result of the depopulation of the C–C double bond involved in the formation of new single bonds), while the last stage corresponds to the non-concerted formation of the two new C–C bonds via the disappearance of the population of the four pseudoradical centers formed in the previous stage. On the other hand, along path a, the first step displays three SSDs, associated with the depopulation of the V(C2,C3) and V(C6,C7) basins, the appearance of the new monosynaptic basins V(C2) and V(C7), and finally the merging of these new monosynaptic basins through the creation of the C2–C7 single bond. The second step is described by a series of five SSDs, that account for the reorganization of the electron density within Int-a via the creation of four pseudoradical centers on the C12, C13, C3 and C6 carbon atoms. The last two SSDs deal with the formation of two C-C bonds via the merging of the monosynaptic basins formed in the previous domains. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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24 pages, 6428 KiB

Open AccessArticle

Designing Electron-Deficient Diketone Unit Based Non-Fused Ring Acceptors with Amplified Optoelectronic Features for Highly Efficient Organic Solar Cells: A DFT Study

by Muhammad Usman Khan, Faiza Shafiq, Sanaa S. Al Abbad, Junaid Yaqoob, Riaz Hussain, Zainab H. A. Alsunaidi, Ghulam Mustafa and Shabbir Hussain

Molecules 2023, 28(8), 3625; https://doi.org/10.3390/molecules28083625 - 21 Apr 2023

Cited by 11 | Viewed by 1699

Abstract

Organic solar cells (OSCs) made of electron-acceptor and electron-donor materials have significantly developed in the last decade, demonstrating their enormous potential in cutting-edge optoelectronic applications. Consequently, we designed seven novel non-fused ring electron acceptors (NFREAs) (BTIC-U1 to BTIC-U7) using synthesized electron-deficient diketone units and reported end-capped acceptors, a viable route for augmented optoelectronic properties. The DFT and TDDFT approaches were used to measure the power conversion efficiency (PCE), open circuit voltage (Voc), reorganization energies (λ_h, λ_e), fill factor (FF), light harvesting efficiency (LHE) and to evaluate the potential usage of proposed compounds in solar cell applications. The findings confirmed that the photovoltaic, photophysical, and electronic properties of the designed molecules BTIC-U1 to BTIC-U7 are superior to those of reference BTIC-R. The TDM analysis demonstrates a smooth flow of charge from the core to the acceptor groups. Charge transfer analysis of the BTIC-U1:PTB7-Th blend revealed orbital superposition and successful charge transfer from HOMO (PTB7-Th) to LUMO (BTIC-U1). The BTIC-U5 and BTIC-U7 outperformed the reference BTIC-R and other developed molecules in terms of PCE (23.29% and 21.18%), FF (0.901 and 0.894), normalized Voc (48.674 and 44.597), and Voc (1.261 eV and 1.155 eV). The proposed compounds enclose high electron and hole transfer mobilities, making them the ideal candidate for use with PTB7-Th film. As a result, future SM-OSC design should prioritize using these constructed molecules, which exhibit excellent optoelectronic properties, as superior scaffolds. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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18 pages, 3061 KiB

Open AccessArticle

Efficient Synthesis of Imine-Carboxylic Acid Functionalized Compounds: Single Crystal, Hirshfeld Surface and Quantum Chemical Exploration

by Muhammad Nawaz Tahir, Akbar Ali, Muhammad Khalid, Muhammad Ashfaq, Mubashir Naveed, Shahzad Murtaza, Iqra Shafiq, Muhammad Adnan Asghar, Raha Orfali and Shagufta Perveen

Molecules 2023, 28(7), 2967; https://doi.org/10.3390/molecules28072967 - 27 Mar 2023

Cited by 17 | Viewed by 2037

Abstract

Two aminobenzoic acid based crystalline imines (HMBA and DHBA) were synthesized through a condensation reaction of 4-aminobenzoic acid and substituted benzaldehydes. Single-crystal X-ray diffraction was employed for the determination of structures of prepared Schiff bases. The stability of super molecular structures of both molecules was achieved by intramolecular H-bonding accompanied by strong, as well as comparatively weak, intermolecular attractive forces. The comparative analysis of the non-covalent forces in HMBA and DHBA was performed by Hirshfeld surface analysis and an interaction energy study between the molecular pairs. Along with the synthesis, quantum chemical calculations were also accomplished at M06/6-311G (d, p) functional of density functional theory (DFT). The frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP), natural bond orbitals (NBOs), global reactivity parameters (GRPs) and natural population (NPA) analyses were also carried out. The findings of FMOs found that E_gap for HMBA was examined to be smaller (3.477 eV) than that of DHBA (3.7933 eV), which indicated a greater charge transference rate in HMBA. Further, the NBO analysis showed the efficient intramolecular charge transfer (ICT), as studied by Hirshfeld surface analysis. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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20 pages, 7914 KiB

Open AccessArticle

Molecular Structure, Electronic Properties, Reactivity (ELF, LOL, and Fukui), and NCI-RDG Studies of the Binary Mixture of Water and Essential Oil of Phlomis bruguieri

by Feride Akman, Azize Demirpolat, Aleksandr S. Kazachenko, Anna S. Kazachenko, Noureddine Issaoui and Omar Al-Dossary

Molecules 2023, 28(6), 2684; https://doi.org/10.3390/molecules28062684 - 16 Mar 2023

Cited by 14 | Viewed by 2750

Abstract

Essential oils are volatile oil-like liquids with a characteristic strong smell and taste. They are formed in plants and are then extracted. Essential oils have extremely strong physiological and pharmacological properties, which are used in the medicine, cosmetics, and food industries. In this study, the molecules caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene, which are the molecules with the highest contents in the essential oil of the plant mentioned in the title, were selected and theoretical calculations describing their interactions with water were performed. Because oil–water mixtures are very important in biology and industry and are ubiquitous in nature, quantum chemical calculations for binary mixtures of water with caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene were performed using the density functional theory (DFT)/B3LYP method with a basis of 6–31 G (d, p). Molecular structures, HOMO–LUMO energies, electronic properties, reactivity (ELF, LOL, and Fukui), and NCI-RDG and molecular electrostatic potential (MEP) on surfaces of the main components of Phlomis bruguieri Desf. essential oil were calculated and described. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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20 pages, 6008 KiB

Open AccessArticle

Molecular Structure, Spectral Analysis, Molecular Docking and Physicochemical Studies of 3-Bromo-2-hydroxypyridine Monomer and Dimer as Bromodomain Inhibitors

by Nizar Lefi, Aleksandr S. Kazachenko, Murugesan Raja, Noureddine Issaoui and Anna S. Kazachenko

Molecules 2023, 28(6), 2669; https://doi.org/10.3390/molecules28062669 - 15 Mar 2023

Cited by 3 | Viewed by 1935

Abstract

In this paper, both methods (DFT and HF) were used in a theoretical investigation of 3-bromo-2-Hydroxypyridine (3-Br-2HyP) molecules where the molecular structures of the title compound have been optimized. Molecular electrostatic potential (MEP) was computed using the B3LYP/6-311++G(d,p) level of theory. The time-dependent density functional theory (TD-DFT) approach was used to simulate the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) on the one hand to achieve the frontier orbital gap and on the other hand to calculate the UV–visible spectrum of the compound in gas phase and for different solvents. In addition, electronic localization function and Fukui functions were carried out. Intermolecular interactions were discussed by the topological AIM (atoms in molecules) approach. The thermodynamic functions have been reported with the help of spectroscopic data using statistical methods revealing the correlations between these functions and temperature. To describe the non-covalent interactions, the reduced density gradient (RDG) analysis is performed. To study the biological activity of the compound of the molecule, molecular docking studies were executed on the active sites of BRD2 inhibitors and to explore the hydrogen bond interaction, minimum binding energies with targeted receptors such as PDB ID: 5IBN, 3U5K, 6CD5 were calculated. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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15 pages, 5016 KiB

Open AccessArticle

Femtosecond Time-Resolved Observation of Relaxation and Wave Packet Dynamics of the S1 State in Electronically Excited o-Fluoroaniline

by Bumaliya Abulimiti, Huan An, Zhenfei Gu, Xulan Deng, Bing Zhang, Mei Xiang and Jie Wei

Molecules 2023, 28(4), 1999; https://doi.org/10.3390/molecules28041999 - 20 Feb 2023

Viewed by 1544

Abstract

Quantum beat frequency is the basis for understanding interference effects and vibrational wave packet dynamics and has important applications. Using femtosecond time-resolved mass spectrometry and femtosecond time-resolved photoelectron image combined with theoretical calculations, we study the electronic excited-state relaxation of o-fluoraniline molecule and the time-dependent evolution of vibrational wave packets between different eigenstates. After the molecule absorbs a photon of 288.3 nm and is excited to the S₁ state, intramolecular vibrational redistribution first occurs on the time scale τ₁ = 349 fs, and then the transition to the triplet state occurs through the intersystem crossing on the time scale τ₂ = 583 ps, and finally, the triplet state occurs decays slowly through the time scale τ₃ = 2074 ps. We find the intramolecular vibrational redistribution is caused by the 0⁰, 10b¹ and 16a¹ vibrational modes of the S_l state origin. That is, the 288.3 nm femtosecond laser excites the molecule to the S₁ state, and the continuous flow of the vibrational wave packet prepares a coherent superposition state of three vibrational modes. Through extracting the oscillation of different peak intensities in the photoelectron spectrum, we observe reversible changes caused by mutual interference of the S₁ 0⁰, S₁ 10b¹ and S₁ 16a¹ states when the wave packets flow. When the pump pulse is 280 nm, the beat frequency disappears completely. This is explained in terms of increases in the vibrational field density and characteristic period of oscillation, and statistical averaging makes the quantum effect smooth and indistinguishable. In addition, the Rydberg component of the S₁ state is more clearly resolved by combining experiment and theory. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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19 pages, 8478 KiB

Open AccessArticle

Energy Level Prediction of Organic Semiconductors for Photodetectors and Mining of a Photovoltaic Database to Search for New Building Units

by Jehad Saleh, Sajjad Haider, Muhammad Saeed Akhtar, Muhammad Saqib, Muqadas Javed, Sayed Elshahat and Ghulam Mustafa Kamal

Molecules 2023, 28(3), 1240; https://doi.org/10.3390/molecules28031240 - 27 Jan 2023

Cited by 6 | Viewed by 2130

Abstract

Due to the large versatility in organic semiconductors, selecting a suitable (organic semiconductor) material for photodetectors is a challenging task. Integrating computer science and artificial intelligence with conventional methods in optimization and material synthesis can guide experimental researchers to develop, design, predict and discover high-performance materials for photodetectors. To find high-performance organic semiconductor materials for photodetectors, it is crucial to establish a relationship between photovoltaic properties and chemical structures before performing synthetic procedures in laboratories. Moreover, the fast prediction of energy levels is desirable for designing better organic semiconductor photodetectors. Herein, we first collected large sets of data containing photovoltaic properties of organic semiconductor photodetectors reported in the literature. In addition, molecular descriptors that make it easy and fast to predict the required properties were used to train machine learning models. Power conversion efficiency and energy levels were also predicted. Multiple models were trained using experimental data. The light gradient boosting machine (LGBM) regression model and Hist gradient booting regression model are the best models. The best models were further tuned to achieve better prediction ability. The reliability of our designed approach was further verified by mining the photovoltaic database to search for new building units. The results revealed that good consistency is obtained between experimental outcomes and model predictions, indicating that machine learning is a powerful approach to predict the properties of photodetectors, which can facilitate their rapid development in various fields. Full article

(This article belongs to the Special Issue Recent Advancements in Density Functional Theory (DFT) and beyond for Computational Chemistry)

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