Research

11 pages, 2653 KiB

Open AccessArticle

Theoretical Study of p-Block Metal Single-Atom-Loaded Carbon Nitride Catalyst for Photocatalytic Water Splitting

by Mengning Chen, Yidi Wu, Qiang Wan and Sen Lin

Molecules 2024, 29(9), 2030; https://doi.org/10.3390/molecules29092030 (registering DOI) - 28 Apr 2024

Graphitic carbon nitride (g-C₃N₄), recognized for its considerable potential as a heterogeneous photocatalyst in water splitting, has attracted extensive research interest. By using density functional theory (DFT) calculations, the regulatory role of p-block metal (PM) single [...] Read more.

Graphitic carbon nitride (g-C₃N₄), recognized for its considerable potential as a heterogeneous photocatalyst in water splitting, has attracted extensive research interest. By using density functional theory (DFT) calculations, the regulatory role of p-block metal (PM) single atoms on the photocatalytic activity of g-C₃N₄ in overall water splitting was systematically explored. The incorporation of PM atoms (Ge, Sn and Pb) led to a reduction in the overpotentials required for both the oxygen evolution reaction (OER) and the hydrogen evolution reaction (HER). Combined with the electronic structures analysis via hybrid functional, it was found that the introduction of Ge, Sn or Pb optimizes the positions of the valence band maximum (VBM) and the conduction band minimum (CBM), providing a robust driving force for HER and ensuring substantial driving force for OER. Meanwhile, the presence of these three PMs induces the spatial separation of VBM and CBM, inhibiting the recombination of carriers. These findings have significant implications for the design and preparation of efficient photocatalysts. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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15 pages, 2980 KiB

Open AccessArticle

Revealing the Critical Role of Global Electron Density Transfer in the Reaction Rate of Polar Organic Reactions within Molecular Electron Density Theory

by Luis R. Domingo and Mar Ríos-Gutiérrez

Molecules 2024, 29(8), 1870; https://doi.org/10.3390/molecules29081870 - 19 Apr 2024

Viewed by 234

Abstract

The critical role of global electron density transfer (GEDT) in increasing the reaction rate of polar organic reactions has been studied within the framework of Molecular Electron Density Theory (MEDT). To this end, the series of the polar Diels–Alder (P-DA) reactions of cyclopentadiene [...] Read more.

The critical role of global electron density transfer (GEDT) in increasing the reaction rate of polar organic reactions has been studied within the framework of Molecular Electron Density Theory (MEDT). To this end, the series of the polar Diels–Alder (P-DA) reactions of cyclopentadiene with cyanoethylene derivatives, for which experimental kinetic data are available, have been chosen. A complete linear correlation between the computed activation Gibbs free energies and the GEDT taking place at the polar transition state structures (TSs) is found; the higher the GEDT at the TS, the lower the activation Gibbs free energy. An interacting quantum atoms energy partitioning analysis allows for establishing a complete linear correlation between the electronic stabilization of the electrophilic ethylene frameworks and the GEDT taking place at the polar TSs. This finding supports Parr’s proposal for the definition of the electrophilicity ω index. The present MEDT study establishes the critical role of the GEDT in the acceleration of polar reactions, since the electronic stabilization of the electrophilic framework with the electron density gain is greater than the destabilization of the nucleophilic one, making a net favorable electronic contribution to the decrease in the activation energy. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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18 pages, 5996 KiB

Open AccessArticle

A Comprehensive Study of Al₂O₃ Mechanical Behavior Using Density Functional Theory and Molecular Dynamics

by Mostafa Fathalian, Eligiusz Postek, Masoud Tahani and Tomasz Sadowski

Molecules 2024, 29(5), 1165; https://doi.org/10.3390/molecules29051165 - 05 Mar 2024

Viewed by 602

Abstract

This study comprehensively investigates Al₂O₃′s mechanical properties, focusing on fracture toughness, surface energy, Young’s modulus, and crack propagation. The density functional theory (DFT) is employed to model the vacancies in Al₂O₃, providing essential insights into [...] Read more.

This study comprehensively investigates Al₂O₃′s mechanical properties, focusing on fracture toughness, surface energy, Young’s modulus, and crack propagation. The density functional theory (DFT) is employed to model the vacancies in Al₂O₃, providing essential insights into this material’s structural stability and defect formation. The DFT simulations reveal a deep understanding of vacancy-related properties and their impact on mechanical behavior. In conjunction with molecular dynamics (MD) simulations, the fracture toughness and crack propagation in Al₂O₃ are explored, offering valuable information on material strength and durability. The surface energy of Al₂O₃ is also assessed using DFT, shedding light on its interactions with the surrounding environment. The results of this investigation highlight the significant impact of oxygen vacancies on mechanical characteristics such as ultimate strength and fracture toughness, drawing comparisons with the effects observed in the presence of aluminum vacancies. Additionally, the research underscores the validation of fracture toughness outcomes derived from both DFT and MD simulations, which align well with findings from established experimental studies. Additionally, the research underscores the validation of fracture toughness outcomes derived from DFT and MD simulations, aligning well with findings from established experimental studies. The combination of DFT and MD simulations provides a robust framework for a comprehensive understanding of Al₂O_3′s mechanical properties, with implications for material science and engineering applications. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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19 pages, 2687 KiB

Open AccessArticle

Probing Non-Covalent Interactions through Molecular Balances: A REG-IQA Study

by Fabio Falcioni, Sophie Bennett, Pallas Stroer-Jarvis and Paul L. A. Popelier

Molecules 2024, 29(5), 1043; https://doi.org/10.3390/molecules29051043 - 28 Feb 2024

Viewed by 583

Abstract

The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe₂ and 2-Y with Y = H, CN, NO₂, OMe, NMe₂) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level [...] Read more.

The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe₂ and 2-Y with Y = H, CN, NO₂, OMe, NMe₂) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level of theory using the energy partitioning method of Interacting Quantum Atoms/Fragments (IQA/IQF). The partitioned energies are analysed by the Relative Energy Gradient (REG) method, which calculates the correlation between these energies and the total energy of a system, thereby explaining the role atoms have in the energetic behaviour of the total system. The traditional “back-of-the-envelope” open and closed conformations of molecular balances do not correspond to those of the lowest energy. Hence, more care needs to be taken when considering which geometries to use for comparison with the experiment. The REG-IQA method shows that the 1-H and 1-OMe balances behave differently to the 1-Me and 1-NMe₂ balances because the latter show more prominent electrostatics between carbonyl groups and undergoes a larger dihedral rotation due to the bulkiness of the functional groups. For the 2-Y balance, REG-IQA shows the same behaviour across the series as the 1-H and 1-OMe balances. From an atomistic point of view, the formation of the closed conformer is favoured by polarisation and charge-transfer effects on the amide bond across all balances and is counterbalanced by a de-pyramidalisation of the amide nitrogen. Moreover, focusing on the oxygen of the amide carbonyl and the α-carbon of the remaining carbonyl group, electrostatics have a major role in the formation of the closed conformer, which goes against the well-known n-π* interaction orbital overlap concept. However, REG-IQF shows that exchange–correlation energies overtake electrostatics for all the 2-Y balances when working with fragments around the carbonyl groups, while they act on par with electrostatics for the 1-OMe and 1-NMe₂. REG-IQF also shows that exchange–correlation energies in the 2-Y balance are correlated to the inductive electron-donating and -withdrawing trends on aromatic groups. We demonstrate that methods such as REG-IQA/IQF can help with the fine-tuning of molecular balances prior to the experiment and that the energies that govern the probed interactions are highly dependent on the atoms and functional groups involved. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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22 pages, 3736 KiB

Open AccessArticle

Formulation Optimization and Performance Prediction of Red Mud Particle Adsorbents Based on Neural Networks

by Longjiang Li, Yalan Wang and Wenyuan Wang

Molecules 2024, 29(5), 970; https://doi.org/10.3390/molecules29050970 - 22 Feb 2024

Cited by 1 | Viewed by 565

Abstract

Red mud (RM), a bauxite residue, contains hazardous radioactive wastes and alkaline material and poses severe surface water and groundwater contamination risks, necessitating recycling. Pretreated RM can be used to make adsorbents for water treatment. However, its performance is affected by many factors, [...] Read more.

Red mud (RM), a bauxite residue, contains hazardous radioactive wastes and alkaline material and poses severe surface water and groundwater contamination risks, necessitating recycling. Pretreated RM can be used to make adsorbents for water treatment. However, its performance is affected by many factors, resulting in a nonlinear correlation and coupling relationship. This study aimed to identify the best formula for an RM adsorbent using a mathematical model that examines the relationship between 11 formulation types (e.g., pore-assisting agent, component modifier, and external binder) and 9 properties (e.g., specific surface area, wetting angle, and Zeta potential). This model was built using a back-propagation neural network (BP) based on single-factor experimental data and orthogonal experimental data. The model trained and predicted the established network structure to obtain the optimal adsorbent formula. The RM particle adsorbents had a pH of 10.16, specific surface area (BET) of 48.92 m²·g⁻¹, pore volume of 2.10 cm³·g⁻¹, compressive strength (ST) of 1.12 KPa, and 24 h immersion pulverization rate (η_m) of 3.72%. In the removal of total phosphorus in flotation tailings backwater, it exhibited a good adsorption capacity (Q) and total phosphorous removal rate (η) of 48.63 mg·g⁻¹ and 95.13%, respectively. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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15 pages, 2525 KiB

Open AccessArticle

An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1

by Mengchen Zhou, Fanyu Zhao, Lan Yu, Jinfeng Liu, Jian Wang and John Z. H. Zhang

Molecules 2024, 29(4), 881; https://doi.org/10.3390/molecules29040881 - 16 Feb 2024

Viewed by 780

Abstract

The major histocompatibility complex (MHC) can recognize and bind to external peptides to generate effective immune responses by presenting the peptides to T cells. Therefore, understanding the binding modes of peptide–MHC complexes (pMHC) and predicting the binding affinity of pMHCs play a crucial [...] Read more.

The major histocompatibility complex (MHC) can recognize and bind to external peptides to generate effective immune responses by presenting the peptides to T cells. Therefore, understanding the binding modes of peptide–MHC complexes (pMHC) and predicting the binding affinity of pMHCs play a crucial role in the rational design of peptide vaccines. In this study, we employed molecular dynamics (MD) simulations and free energy calculations with an Alanine Scanning with Generalized Born and Interaction Entropy (ASGBIE) method to investigate the protein–peptide interaction between HLA-A*02:01 and the G9₂₀₉ peptide derived from the melanoma antigen gp100. The energy contribution of individual residue was calculated using alanine scanning, and hotspots on both the MHC and the peptides were identified. Our study shows that the pMHC binding is dominated by the van der Waals interactions. Furthermore, we optimized the ASGBIE method, achieving a Pearson correlation coefficient of 0.91 between predicted and experimental binding affinity for mutated antigens. This represents a significant improvement over the conventional MM/GBSA method, which yields a Pearson correlation coefficient of 0.22. The computational protocol developed in this study can be applied to the computational screening of antigens for the MHC1 as well as other protein–peptide binding systems. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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18 pages, 3303 KiB

Open AccessArticle

Confining He Atoms in Diverse Ice-Phases: Examining the Stability of He Hydrate Crystals through DFT Approaches

by Raquel Yanes-Rodríguez and Rita Prosmiti

Molecules 2023, 28(23), 7893; https://doi.org/10.3390/molecules28237893 - 01 Dec 2023

Viewed by 886

Abstract

In the realm of solid water hydrostructures, helium atoms have a tendency to occupy the interstitial spaces formed within the crystal lattice of ice structures. The primary objective of this study is to examine the stability of various ice crystals when influenced by [...] Read more.

In the realm of solid water hydrostructures, helium atoms have a tendency to occupy the interstitial spaces formed within the crystal lattice of ice structures. The primary objective of this study is to examine the stability of various ice crystals when influenced by the presence of He atoms. Presenting a first attempt at a detailed computational description of the whole energy components (guest–water, water–water, guest–guest) in the complete crystal unit cells contributes to enhancing the knowledge available about these relatively unexplored helium–water systems, which could potentially benefit future experiments. For this purpose, two different ice structures were considered: the previously established He@ice II system, and the predicted (but currently nonexistent) He@ice XVII system. One of the main features of these He-filled structures is the stability conferred by the weak van der Waals dispersion forces that occur between the host lattice and the guest atoms, in addition to the hydrogen bonds established among the water molecules. Hence, it is crucial to accurately describe these interactions. Therefore, the first part of this research is devoted examining the performance and accuracy of various semi-local and non-local DFT/DFT-D functionals, in comparison with previous experimental and/or high-level computational data. Once the best-performing DFT functional has been identified, the stability of these empty and He-filled structures, including different number of He atoms within the lattices, is analysed in terms of their structural (lattice deformation), mechanical (pressure compression effects) and energetic properties (binding and saturation energies). In this manner, the potential formation of these structures under zero temperature and pressure conditions can be evaluated, while their maximum storage capacity is also determined. The obtained results reveal that, despite the weak underlying interactions, the He encapsulation has a rather notable effect on both lattice parameters and energetics, and therefore, the guest–host interactions are far from being negligible. Besides, both ice crystals are predicted to remain stable when filled with He atoms, with ice XVII exhibiting a higher capacity for accommodating a larger number of guest atoms within its interstitial spaces. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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13 pages, 1514 KiB

Open AccessArticle

Calculation of Mechanical Properties, Electronic Structure and Optical Properties of CsPbX₃ (X = F, Cl, Br, I)

by Yang Liu, Canxiang Fang, Shihe Lin, Gaihui Liu, Bohang Zhang, Huihui Shi, Nan Dong, Nengxun Yang, Fuchun Zhang, Xiang Guo and Xinghui Liu

Molecules 2023, 28(22), 7643; https://doi.org/10.3390/molecules28227643 - 17 Nov 2023

Viewed by 885

Abstract

We utilized a first-principle density functional theory for a comprehensive analysis of CsPbX₃ (X = F, Cl, Br, I) to explore its physical and chemical properties, including its mechanical behavior, electronic structure and optical properties. Calculations show that all four materials have [...] Read more.

We utilized a first-principle density functional theory for a comprehensive analysis of CsPbX₃ (X = F, Cl, Br, I) to explore its physical and chemical properties, including its mechanical behavior, electronic structure and optical properties. Calculations show that all four materials have good stability, modulus of elasticity, hardness and wear resistance. Additionally, CsPbX₃ demonstrates a vertical electron leap and serves as a semiconductor material with direct band gaps of 3.600 eV, 3.111 eV, 2.538 eV and 2.085 eV. In examining its optical properties, we observed that the real and imaginary components of the dielectric function exhibit peaks within the low-energy range. Furthermore, the dielectric function gradually decreases as the photon energy increases. The absorption spectrum reveals that the CsPbX₃ material exhibits the highest UV light absorption, and as X changes (with the increase in atomic radius within the halogen group of elements), the light absorption undergoes a red shift, becoming stronger and enhancing light utilization. These properties underscore the material’s potential for application in microelectronic and optoelectronic device production. Moreover, they provide a theoretical reference for future investigations into CsPbX₃ materials. Full article

(This article belongs to the Special Issue Feature Papers in Computational and Theoretical Chemistry)

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