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Application of Computer Simulation in Materials Science of Molecules

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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 (31 August 2023) | Viewed by 22660

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Special Issue Editor

Prof. Dr. Li Yang

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Guest Editor

School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
Interests: computer simulations; nanomaterials; biomaterials; composites; catalysts; surfaces; interfaces
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Special Issue publishes papers on applications of computer simulations in materials spanning multidisciplinary fields, such as chemistry, biology, and engineering. The materials include nanomaterials, biomaterials, composites, catalysts, surfaces, and interfaces. The computing methods widely cover first principle calculations, molecular dynamics, and statistical mechanics. The theoretical studies focus on the understanding of materials with novel electronic structure, optical, electrical, magnetic, catalytic, and mechanical properties at the atomic level.

The scope of this issue includes but is not limited to:

Designing new materials for energy, catalysis, biology, and other applications;
Understanding the structure, property, performance relationships and their underlying mechanisms;
Developing new computer programs for studying materials.

Prof. Dr. Li Yang
Guest Editor

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Keywords

computer simulations
nanomaterials
biomaterials
composites
catalysts
surfaces
interfaces

Related Special Issue

Application of Computer Simulation in Materials Science of Molecules II in Molecules

Published Papers (11 papers)

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Research

12 pages, 4167 KiB

Open AccessArticle

Mechanistic Study on Steric Activity Interplay of Olefin/Polar Monomers for Industrially Selective Late Transition Metal Catalytic Reactions

by Andleeb Mehmood, Ayyaz Mahmood, Najla AlMasoud, Arzoo Hassan, Taghrid S. Alomar, Zeinhom M. El-Bahy, Nadeem Raza, Xiaoqing Tian and Naeem Ullah

Molecules 2023, 28(20), 7148; https://doi.org/10.3390/molecules28207148 - 18 Oct 2023

Cited by 1 | Viewed by 839

Abstract

A significant issue in developing metal-catalyzed plastic polymer materials is obtaining distinctive catalytic characteristics to compete with current plastics in industrial commodities. We performed first-principle DFT calculations on the key insertion steps for industrially important monomers, vinyl fluoride (VF) and 3,3,3-trifluoropropene (TFP), to explain how the ligand substitution patterns affect the complex’s polymerization behaviors. Our results indicate that the favorable 2,1-insertion of TFP is caused by less deformation in the catalyst moiety of the complexes in contrast to the 1,2-insertion mode. In contrast to the VF monomer, the additional interaction between the fluorine atoms of 3,3,3-trifluoropropene and the carbons of the catalyst ligands also contributed to favor the 2,1-insertion. It was found that the regioselectivity of the monomer was predominated by the progressive alteration of the catalytic geometry caused by small dihedral angles that were developed after the ligand–monomer interaction. Based on the distribution of the 1,2- and 2,1-insertion products, the activity and selectivity were influenced by the steric environment surrounding the palladium center; thus, an increased steric bulk visibly improved the selectivity of the bulkier polar monomer (TFP) during the copolymerization mechanism. In contrast, better activity was maintained through a sterically less hindered Pd metal center; the calculated moderate energy barriers showed that a catalyst with less steric hindrance might provide an opportunity for a wide range of prospective industrial applications. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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23 pages, 4054 KiB

Open AccessArticle

Experimental and Computational Study on Inhibitory Effect and Adsorption Properties of N-Acetylcysteine Amino Acid in Acid Environment

by Adriana Samide, Aurelian Dobriţescu, Cristian Tigae, Cezar Ionuţ Spînu and Bogdan Oprea

Molecules 2023, 28(19), 6799; https://doi.org/10.3390/molecules28196799 - 25 Sep 2023

Cited by 1 | Viewed by 881

Abstract

Potentiodynamic polarization (PDP) and electrochemical impedance spectroscopy (EIS) were applied to study the inhibitory effect of N-acetylcysteine (NAC) on corrosion inhibition of carbon steel in hydrochloric acid solution. N-acetylcysteine influenced the iron dissolution to a greater extent than the hydrogen evolution reaction acting as a mixed inhibitor, predominantly anodic. The charge transfer resistance (R_ct) gradually increased with the inhibitor concentration. From both methods, the inhibition efficiency (IE) reached a value of 89 ± 1% and NAC adsorption followed the Temkin isotherm. The value of adsorption Gibbs energy (Δ

G_{ads}^{o}

), around −35 kJ mol⁻¹, indicated a spontaneous adsorption and mixed action mechanism, with NAC chemical adsorption prevailing over physical one. New data will be reported by the computational study, that was performed using the density functional theory (DFT) method in aqueous phase. Quantum chemical descriptors were determined by B3LYP theory level with 6–31G+(d) basis set. Metropolis Monte Carlo atomistic simulation was used to reveal the adsorption configuration and interactions between acetylcysteine molecules and the carbon steel surface. Theoretical results were consistent with the experimental data, showing that the inhibitor action mechanism consisted of mainly chemisorption of its molecules on the carbon steel surface accompanied by van der Waals forces and electrostatic interactions. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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17 pages, 6098 KiB

Open AccessArticle

Molecular Dynamics Simulation of Polyacrylamide Adsorption on Calcite

by Keat Yung Hue, Jin Hau Lew, Maung Maung Myo Thant, Omar K. Matar, Paul F. Luckham and Erich A. Müller

Molecules 2023, 28(17), 6367; https://doi.org/10.3390/molecules28176367 - 31 Aug 2023

Cited by 3 | Viewed by 1427

Abstract

In poorly consolidated carbonate rock reservoirs, solids production risk, which can lead to increased environmental waste, can be mitigated by injecting formation-strengthening chemicals. Classical atomistic molecular dynamics (MD) simulation is employed to model the interaction of polyacrylamide-based polymer additives with a calcite structure, which is the main component of carbonate formations. Amongst the possible calcite crystal planes employed as surrogates of reservoir rocks, the (1 0 4) plane is shown to be the most suitable surrogate for assessing the interactions with chemicals due to its stability and more realistic representation of carbonate structure. The molecular conformation and binding energies of pure polyacrylamide (PAM), hydrolysed polyacrylamide in neutral form (HPAM), hydrolysed polyacrylamide with 33% charge density (HPAM 33%) and sulfonated polyacrylamide with 33% charge density (SPAM 33%) are assessed to determine the adsorption characteristics onto calcite surfaces. An adsorption-free energy analysis, using an enhanced umbrella sampling method, is applied to evaluate the chemical adsorption performance. The interaction energy analysis shows that the polyacrylamide-based polymers display favourable interactions with the calcite structure. This is attributed to the electrostatic attraction between the amide and carboxyl functional groups with the calcite. Simulations confirm that HPAM33% has a lower free energy than other polymers, presumably due to the presence of the acrylate monomer in ionised form. The superior chemical adsorption performance of HPAM33% agrees with Atomic Force Microscopy experiments reported herein. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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15 pages, 1574 KiB

Open AccessArticle

Bubble Relaxation Dynamics in Homopolymer DNA Sequences

by Malcolm Hillebrand, George Kalosakas, Alan R. Bishop and Charalampos Skokos

Molecules 2023, 28(3), 1041; https://doi.org/10.3390/molecules28031041 - 20 Jan 2023

Viewed by 1146

Abstract

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine–thymine (AT) and guanine–cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule’s dynamics, for times between 0.5–500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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17 pages, 7985 KiB

Open AccessArticle

Functional Regulation of ZnAl-LDHs and Mechanism of Photocatalytic Reduction of CO₂: A DFT Study

by Dongcun Xu, Gang Fu, Zhongming Li, Wenqing Zhen, Hongyi Wang, Meiling Liu, Jianmin Sun, Jiaxu Zhang and Li Yang

Molecules 2023, 28(2), 738; https://doi.org/10.3390/molecules28020738 - 11 Jan 2023

Cited by 3 | Viewed by 2200

Abstract

Defect engineering and heteroatom doping can significantly enhance the activity of zinc-aluminum layered double hydroxides (ZnAl-LDHs) in photocatalytic CO₂ reduction to fuel. However, the in-depth understanding of the associated intrinsic mechanisms is limited. Herein, we systematically investigated Zn vacancies (V_Zn), oxygen vacancies (V_O), and Cu doping on the geometry and electronic structure of ZnAl-LDH using density functional theory (DFT). We also revealed the related reaction mechanism. The results reveal the concerted roles of V_O, V_Zn, and doped-Cu facilitate the formation of the unsaturated metal complexes (Zn^δ+-V_O and Cu^δ+-V_O). They can localize the charge density distribution, function as new active centers, and form the intermediate band. Simultaneously, the intermediate band of functionalized ZnAl-LDHs narrows the band gap and lowers the band edge location. Therefore, it can broaden the absorption range of light and improve the selectivity of CO. Additionally, the unsaturated metal complex lowers the Gibbs free energy barrier for effective CO₂ activation by bringing the d-band center level closer to the Fermi level. The work provided guidance for developing LDH photocatalysts with high activity and selectivity. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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13 pages, 3258 KiB

Open AccessArticle

A Mechanistic Study of Asymmetric Transfer Hydrogenation of Imines on a Chiral Phosphoric Acid Derived Indium Metal-Organic Framework

by Xu Li, Ting Fan, Qingji Wang and Tongfei Shi

Molecules 2022, 27(23), 8244; https://doi.org/10.3390/molecules27238244 - 26 Nov 2022

Cited by 2 | Viewed by 1362

Abstract

A density functional theory (DFT) study is reported to examine the asymmetric transfer hydrogenation (ATH) of imines catalyzed by an indium metal-organic framework (In-MOF) derived from a chiral phosphoric acid (CPA). It is revealed that the imine and reducing agent (i.e., thiazoline) are simultaneously adsorbed on the CPA through H-bonding to form an intermediate, subsequently, a proton is transferred from thiazoline to imine. The transition state TS-R and TS-S are stabilized on the CPA via H-bonding. Compared to the TS-S, the TS-R has shorter H-bonding distances and longer C-H···π distances, it is more stable and experiences less steric hindrance. Consequently, the TS-R exhibits a lower activation barrier affording to the (R)-enantiomer within 68.1% ee in toluene. Imines with substituted groups such as −NO₂, −F, and −OCH₃ are used to investigate the substitution effects on the ATH. In the presence of an electron-withdrawing group like −NO₂, the electrophilicity of imine is enhanced and the activation barrier is decreased. The non-covalent interactions and activation-strain model (ASM) analysis reveal that the structural distortions and the differential noncovalent interactions of TSs in a rigid In-MOF provide the inherent driving force for enantioselectivity. For −OCH₃ substituted imine, the TS-S has the strongest steric hindrance, leading to the highest enantioselectivity. When the solvent is changed from toluene to dichloromethane, acetonitrile, and dimethylsulfoxide with increasing polarity, the activation energies of transition state increase whereas their difference decreases. This implies the reaction is slowed down and the enantioselectivity becomes lower in a solvent of smaller polarity. Among the four solvents, toluene turns out to be the best for the ATH. The calculated results in this study are in fairly good agreement with experimental observations. This study provides a mechanistic understanding of the reaction mechanism, as well as substitution and solvent effects on the activity and enantioselectivity of the ATH. The microscopic insights are useful for the development of new chiral MOFs toward important asymmetric reactions. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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12 pages, 3101 KiB

Open AccessArticle

Synergistic Effects of B-F/B-S and Nitrogen Vacancy Co-Doping on g-C₃N₄ and Photocatalytic CO₂ Reduction Mechanisms: A DFT Study

by Gang Fu, Xiaozhuo Song, Siwei Zhao and Jiaxu Zhang

Molecules 2022, 27(21), 7611; https://doi.org/10.3390/molecules27217611 - 6 Nov 2022

Cited by 3 | Viewed by 1797

Abstract

Nonmetallic co-doping and surface hole construction are simple and efficient strategies for improving the photocatalytic activity and regulating the electronic structure of g-C₃N₄. Here, the g-C₃N₄ catalysts with B-F or B-S co-doping combined with nitrogen vacancies (N_v) are designed. Compared to the pristine g-C₃N₄, the direction of the excited electron orbit for the B-F-co-doped system is more matching (N_2pz→C_2pz), facilitating the separation of electrons and holes. Simultaneously, the introduced nitrogen vacancy can further reduce the bandgap by generating impurity states, thus improving the utilization rate of visible light. The doped S atoms can also narrow the bandgap of the B-S-N_v-co-doped g-C₃N₄, which originates from the p-orbital hybridization between C, N, and S atoms, and the impurity states are generated by the introduction of N vacancies. The doping of B-F-N_v and B-S-N_v exhibits a better CO₂ reduction activity with a reduced barrier for the rate-determining step of around 0.2 eV compared to g-C₃N₄. By changing F to S, the origin of the rate-determining step varies from *CO₂→*COOH to *HCHO→*OCH₃, which eventually leads to different products of CH₃OH and CH₄, respectively. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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14 pages, 3333 KiB

Open AccessArticle

Improving Catalytic Activity of “Janus” MoSSe Based on Surface Interface Regulation

by Mingqian Wang, Xin Wang, Ming Zheng and Xin Zhou

Molecules 2022, 27(18), 6038; https://doi.org/10.3390/molecules27186038 - 16 Sep 2022

Cited by 5 | Viewed by 1847

Abstract

The monolayer Janus MoSSe is considered to be a promising catalytic material due to its unique asymmetric structure. In order to improve its catalytic performance for hydrogen evolution reactions (HERs) and oxygen evolution reactions (OERs), many attempts have been made. In this work, a series of transition metal (TM) atoms were anchored on the Janus MoSSe surface to screen effective TM single-atom catalysts for HERs and OERs through density functional theory (DFT) calculations. Fe@MoSSe presents excellent HERs performance and Ni@MoSSe presents excellent catalytic performance for OERs with extremely low over-potential of 0.32 V. The enhanced activity is attributed to the modest energy level of the d band center of the transition metal atom, and the transition metal atom improves the conductivity of the original MoSSe and offers unoccupied states near the Fermi level. At the same time, the anchoring of transition metal atoms redistributes the charge in the MoSSe system, which effectively regulates the electronic structure of the material itself. The strain calculation shows that the activity of the catalyst can be improved by reasonably adjusting the value of the applied strain. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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12 pages, 3490 KiB

Open AccessArticle

Al-Decorated C₂N Monolayer as a Potential Catalyst for NO Reduction with CO Molecules: A DFT Investigation

by Xinmiao Liu, Yunjie Xu and Li Sheng

Molecules 2022, 27(18), 5790; https://doi.org/10.3390/molecules27185790 - 7 Sep 2022

Cited by 4 | Viewed by 1362

Abstract

Developing efficient and economical catalysts for NO reduction is of great interest. Herein, the catalytic reduction of NO molecules on an Al-decorated C₂N monolayer (Al-C₂N) is systematically investigated using density functional theory (DFT) calculations. Our results reveal that the Al-C₂N catalyst is highly selective for NO, more so than CO, according to the values of the adsorption energy and charge transfer. The NO reduction reaction more preferably undergoes the (NO)₂ dimer reduction process instead of the NO direct decomposition process. For the (NO)₂ dimer reduction process, two NO molecules initially co-adsorb to form (NO)₂ dimers, followed by decomposition into N₂O and O_ads species. On this basis, five kinds of (NO)₂ dimer structures that initiate four reaction paths are explored on the Al-C₂N surface. Particularly, the cis-(NO)₂ dimer structures (D_cis-N and D_cis-O) are crucial intermediates for NO reduction, where the max energy barrier along the energetically most favorable pathway (path II) is as low as 3.6 kcal/mol. The remaining O_ads species on Al-C₂N are then easily reduced with CO molecules, being beneficial for a new catalytic cycle. These results, combined with its low-cost nature, render Al-C₂N a promising catalyst for NO reduction under mild conditions. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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15 pages, 3594 KiB

Open AccessArticle

Theoretical Study on the High HER/OER Electrocatalytic Activities of 2D GeSi, SnSi, and SnGe Monolayers and Further Improvement by Imposing Biaxial Strain or Doping Heteroatoms

by Cuimei Li, Guangtao Yu, Xiaopeng Shen, Ying Li and Wei Chen

Molecules 2022, 27(16), 5092; https://doi.org/10.3390/molecules27165092 - 10 Aug 2022

Cited by 6 | Viewed by 4578

Abstract

Under the DFT calculations, two-dimensional (2D) GeSi, SnSi, and SnGe monolayers, considered as the structural analogues of famous graphene, are confirmed to be dynamically, mechanically and thermodynamically stable, and all of them can also possess good conductivity. Furthermore, we systematically investigate their electrocatalytic activities in overall water splitting. The SnSi monolayer can show good HER catalytic activity, while the SnGe monolayer can display remarkable OER catalytic activity. In particular, the GeSi monolayer can even exhibit excellent bifunctional HER/OER electrocatalytic activities. In addition, applying the biaxial strain or doping heteroatoms (especially P atom) can be regarded as the effective strategies to further improve the HER activities of these three 2D monolayers. The doped GeSi and SnSi systems can usually exhibit higher HER activity than the doped SnGe systems. The correlative catalytic mechanisms are also analyzed. This work could open up a new avenue for the development of non-noble-metal-based HER/OER electrocatalysts. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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14 pages, 3639 KiB

Open AccessArticle

Application of Deep Learning Workflow for Autonomous Grain Size Analysis

by Alexandre Bordas, Jingchao Zhang and Juan C. Nino

Molecules 2022, 27(15), 4826; https://doi.org/10.3390/molecules27154826 - 28 Jul 2022

Cited by 4 | Viewed by 3963

Abstract

Traditional grain size determination in materials characterization involves microscopy images and a laborious process requiring significant manual input and human expertise. In recent years, the development of computer vision (CV) has provided an alternative approach to microstructural characterization with preliminary implementations greatly simplifying the grain size determination process. Here, an end-to-end workflow to measure grain size in microscopy images without any manual input is presented. Following the ASTM standards for grain size determination, results from the line intercept (Heyn’s method) and planimetric (Saltykov’s method) approaches are used as the baseline. A pre-trained holistically nested edge detection (HED) model is used for CV-based edge detection, and the results are further compared to the classic Canny edge detection method. Post-processing was performed using open-source image processing packages to extract the grain size. In optical microscope images, the pre-trained HED model achieves much higher accuracy than the Canny edge detection method while reducing the image processing time by one to two orders of magnitude compared to traditional methods. The effects of morphological operations on the predicted grain size accuracy are also explored. Overall, the proposed end-to-end convolutional neural network (CNN)-based workflow can significantly reduce the processing time while maintaining the same accuracy as the traditional manual method. Full article

(This article belongs to the Special Issue Application of Computer Simulation in Materials Science of Molecules)

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