Computational and Theoretical Chemistry最新文献_第4页

First-principles study of transition metal atom doped MoS2 as single-atom electrocatalysts for nitrogen fixation

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2025.115090

Wei Song , Zhe Fu , Jiale Liu , Jinqiang Li , Chaozheng He

{"title":"First-principles study of transition metal atom doped MoS2 as single-atom electrocatalysts for nitrogen fixation","authors":"Wei Song , Zhe Fu , Jiale Liu , Jinqiang Li , Chaozheng He","doi":"10.1016/j.comptc.2025.115090","DOIUrl":"10.1016/j.comptc.2025.115090","url":null,"abstract":"<div><div>NH<sub>3</sub>, as a carbon-free energy carrier that can replace H<sub>2</sub>, is also an important raw material for fertilizer. Compared with Haber–Bosch process, electrocatalytic NH<sub>3</sub> synthesis has the green advantage of using renewable resources under ambient conditions. Herein, the catalytic performance of 3d transition metal single atom anchored in MoS<sub>2</sub> (TM@MoS<sub>2</sub>) as electrocatalyst for nitrogen reduction reaction (NRR) has been investigated by first-principles calculation. By evaluating the stability, activity and selectivity of the catalysts, V@MoS<sub>2</sub> was found to be a potential catalyst. After simulating the entire NRR pathway, it was found that the limiting potential was only −0.311 V, indicating that V@MoS<sub>2</sub> had high catalytic activity. Finally, the partial density of states, charge density difference and crystal orbital Hamilton population were calculated to reveal the reason for the high catalytic activity of V@MoS<sub>2</sub>. We hope that this work can provide new design concepts for the development of efficient MoS<sub>2</sub>-based electrocatalysts.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115090"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A DFT study of doped first-row transition metals on Si12C12 nanocages as promising nanosensors for detecting volatile amines of fish spoilage

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2024.115051

Indah Miftakhul Janah , Reka Mustika Sari , Faris Hermawan , Aulia Sukma Hutama , Lala Adetia Marlina

{"title":"A DFT study of doped first-row transition metals on Si12C12 nanocages as promising nanosensors for detecting volatile amines of fish spoilage","authors":"Indah Miftakhul Janah , Reka Mustika Sari , Faris Hermawan , Aulia Sukma Hutama , Lala Adetia Marlina","doi":"10.1016/j.comptc.2024.115051","DOIUrl":"10.1016/j.comptc.2024.115051","url":null,"abstract":"<div><div>This study explores the potential of transition metal-doped Si<sub>12</sub>C<sub>12</sub> nanocages for detecting volatile amines released during fish spoilage, using density functional theory (ωB97XD). The analysis focuses on structural stability, electronic properties, adsorption mechanisms, thermodynamics, sensitivity, and selectivity. Results indicate that TM doping enhances the adsorption of amines, with most interactions being spontaneous and exothermic. The trimethylamine∙∙∙TiSi<sub>11</sub>C<sub>12</sub> complex exhibits particularly favorable thermodynamic properties. Sensitivity tests reveal that Cr, Cu, and Zn-doped nanocages demonstrate high responsiveness to trimethylamine at room temperature, with significant electronic property shifts upon adsorption. These findings highlight the potential of TM-doped Si<sub>12</sub>C<sub>12</sub> nanocages as effective, selective, and sensitive sensors for monitoring volatile amines, aiding food quality control and fish freshness assessment. The study provides a theoretical basis for designing Si<sub>12</sub>C<sub>12</sub>-based gas sensors, contributing to advancements in food safety technology.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115051"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unravelling the mechanism of tyrosinase inhibition by arylpiperidine and arylpiperazine derivatives: A computational approach

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2025.115085

Lucas Sousa Martins , Beatriz Alves Bentes , Tricia Naicker , Thavendran Govender , Hendrik Gerhardus Kruger , Cláudio Nahum Alves , Jerônimo Lameira , José Rogério A. Silva

{"title":"Unravelling the mechanism of tyrosinase inhibition by arylpiperidine and arylpiperazine derivatives: A computational approach","authors":"Lucas Sousa Martins , Beatriz Alves Bentes , Tricia Naicker , Thavendran Govender , Hendrik Gerhardus Kruger , Cláudio Nahum Alves , Jerônimo Lameira , José Rogério A. Silva","doi":"10.1016/j.comptc.2025.115085","DOIUrl":"10.1016/j.comptc.2025.115085","url":null,"abstract":"<div><div>Melanogenesis produces human melanin, which protects against UV radiation but can lead to skin issues and severe cancers if not appropriately regulated. The enzyme tyrosinase (TYR) plays a crucial role in melanin production, so inhibiting it is an essential target for controlling melanin levels. This study applied classical and quantum computational methods to examine how TYR interacts with inhibitors based on arylpiperidine and arylpiperazine. Using classical molecular dynamics (MD) simulations and the Linear Interaction Energy (LIE) method, we identified a strong correlation (<em>r</em><sup>2</sup> = 0.963) between computational and experimental binding free energies, underscoring the accuracy of these approaches. Additionally, residual decomposition analysis revealed the critical role of electrostatic interactions with Cu<sup>2+</sup> ions at the active site, along with van der Waals interactions involving key residues, including Phe197, Pro201, Val218, Asn205, and Arg209, which are pivotal for inhibitor effectiveness. These findings are further supported by Free Energy Perturbation (FEP) calculations, which demonstrate excellent agreement with experimental data (<em>r</em><sup>2</sup> = 0.843), providing robust validation of the computational models. Additionally, quantum mechanical (QM) calculations using the DFT (wB97XD/6-311++G(d,p)) method uncovered electronic factors that influence inhibitor binding. Analyzing the frontier molecular orbitals (FMOs) and QM descriptors for L04, L08 and L19 inhibitors provided insights into TYR binding by arylpiperidine and arylpiperazine-based compounds. This thorough computational analysis improves our understanding of TYR inhibition and helps guide the development of treatments for conditions related to melanogenesis.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115085"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oxygen evolution reaction mechanism on platinum dioxide surfaces based on density functional theory calculations

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2024.115020

Xiru Cao, Zhibin Tan, Chen Ji, Changwei Pan

{"title":"Oxygen evolution reaction mechanism on platinum dioxide surfaces based on density functional theory calculations","authors":"Xiru Cao, Zhibin Tan, Chen Ji, Changwei Pan","doi":"10.1016/j.comptc.2024.115020","DOIUrl":"10.1016/j.comptc.2024.115020","url":null,"abstract":"<div><div>The oxygen evolution reaction (OER) counterbalances the hydrogen evolution reaction (HER) during water dissociation under an electric field. Platinum (Pt) group metals and their oxides exhibit considerable durability as electrocatalysts for water dissociation. However, an atomic-level understanding of the OER on Pt-oxide surfaces at high potential remains elusive because of the limited experimental techniques for tracking dynamic surface species involved in adsorption, electron transfer, or interactions. Herein, the OER mechanisms involving water nucleophilic attack (WNA) and intramolecular oxygen coupling (IMOC) were studied on Pt and platinum dioxide (PtO<sub>2</sub>) surfaces using density functional theory (DFT) calculations, indicating that the WNA mechanism dominates the OER on Pt and PtO<sub>2</sub> electrode surfaces. The OER activity on the PtO<sub>2</sub>(100) surface is better than the PtO<sub>2</sub>(111) surface due to the high overpotential obtained on PtO<sub>2</sub>(111). These findings offer valuable insights into the OER mechanism on oxidized Pt surfaces and suggest new strategies for designing and optimizing Pt-based catalysts for improved stability and performance.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115020"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A mechanistic study of CO oxidation on PdO(1 0 1) surface

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2024.115037

Chengcheng Ao , Chunlan Qin , Lidong Zhang , Shanshan Ruan

引用次数: 0

First-principles calculations to investigate Electronic, half-metallicity, thermodynamics, thermoelectric and mechanical properties of new Half-Heusler alloys FeCoZ (Z = Si, Ge, and Pb)

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2025.115066

Maryam Touqir , G. Murtaza , Ahmad Ayyaz , Ahmad Usman , M.Basit Shakir , Saba Saleem , Hummaira khan , Muhammad Umair Ashraf , Khalid M. Elhindi

{"title":"First-principles calculations to investigate Electronic, half-metallicity, thermodynamics, thermoelectric and mechanical properties of new Half-Heusler alloys FeCoZ (Z = Si, Ge, and Pb)","authors":"Maryam Touqir , G. Murtaza , Ahmad Ayyaz , Ahmad Usman , M.Basit Shakir , Saba Saleem , Hummaira khan , Muhammad Umair Ashraf , Khalid M. Elhindi","doi":"10.1016/j.comptc.2025.115066","DOIUrl":"10.1016/j.comptc.2025.115066","url":null,"abstract":"<div><div>FeCoZ compounds (where Z = Si, Ge, or Pb) are essential for spintronics and thermoelectric applications. This study, using density functional theory and PBE-GGA for exchange–correlation, explores their structural, electrical, magnetic, thermoelectric, thermodynamic, and elastic properties. Density of states analysis and spin-polarized band structures indicate that all three compounds have an indirect bandgap in the spin-up (↑) channel and are metallic in the spin-down (↓) channel. The exchange mechanism is finally produced by splitting the degeneracy of Co’s 3d-states via the John-Teller distortion. Ferromagnetic stability in FeCoZ (Z = Si, Ge, or Pb) is shown by negative N<sub>o</sub>α and N<sub>o</sub>β values. Thermoelectric properties are derived using the BoltzTraP method. The increasing PF in alloys indicates their potential use in high-temperature thermoelectric applications. Consequently, the elevated ZT value produced in the spin-up condition indicates that these alloys are suitable for thermoelectric applications, and the quasi-harmonic Debye model indicates thermodynamic stability. Poisson’s ratio, Pugh’s ratio, and Cauchy’s pressure confirm mechanical stability and ductility. Overall, these compounds, suited for spintronic applications, exhibit half-metallicity, ferromagnetism, and high intrinsic magnetic moments.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115066"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A first principle study of Nitrogen/Carbon replacement in a set of β-aminoacrolein/β-thioaminoacrolein derivatives

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2024.115053

Malihe Shahraki, Alireza Nowroozi, Ebrahim Nakhaei

{"title":"A first principle study of Nitrogen/Carbon replacement in a set of β-aminoacrolein/β-thioaminoacrolein derivatives","authors":"Malihe Shahraki, Alireza Nowroozi, Ebrahim Nakhaei","doi":"10.1016/j.comptc.2024.115053","DOIUrl":"10.1016/j.comptc.2024.115053","url":null,"abstract":"<div><div>This study systematically investigates the impact of N/C substitution in β-aminoacrolein/β-thioaminoacrolein derivatives at various theoretical levels. Key electronic energy components, including electron configuration, nitrogen atom positioning, lone pair-lone pair (Lp-Lp) repulsion, and resonance-assisted hydrogen bonding (RAHB), are evaluated. Results reveal that electron configuration contributes the most stabilizing energy (∼-16 Hartree), while nitrogen positioning and Lp-Lp repulsions destabilizes structures, following the trend: N2 < N1 < N3. RAHB energies are strongly influenced by nitrogen count, with stability improving in the order: N1 (−0.0145) < N2 (−0.0273) < N3 (−0.0370) < N1N2 (−0.0418) < N1N3 (−0.0515) < N2N3 (−0.0643) < N1N2N3 (-0.0788H). Furthermore, energetic, structural, spectral, and topological descriptors support these findings. Interestingly, the aromaticity index indicates a slight reduction in π-electron delocalization (π-ED) with N/C substitution, challenging conventional RAHB theory.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115053"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Influence of external electric field regulating hydrogen adsorption on graphene quantum dots, graphene quantum dots with defects, and metal-ion-doped graphene quantum dots

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2024.115050

Thanawit Kuamit , Fadjar Mulya , Sirilak Kongkaew , Vudhichai Parasuk

{"title":"Influence of external electric field regulating hydrogen adsorption on graphene quantum dots, graphene quantum dots with defects, and metal-ion-doped graphene quantum dots","authors":"Thanawit Kuamit , Fadjar Mulya , Sirilak Kongkaew , Vudhichai Parasuk","doi":"10.1016/j.comptc.2024.115050","DOIUrl":"10.1016/j.comptc.2024.115050","url":null,"abstract":"<div><div>Hydrogen storage is crucial for efficient hydrogen energy utilization, but current materials often require extreme conditions, such as low temperatures (<20.15 K) or high pressures (350–700 atm), and an ideal adsorption energy between −0.2 and −0.6 eV. This study employs density functional theory (DFT) to explore hydrogen adsorption on graphene quantum dots (GQDs), including pristine GQDs, nitrogen-substituted divacancy defect GQDs (4N-GQDs), and metal-ion-doped 4N-GQDs (M-4N-GQDs, M = Ti<sup>2+</sup>, Fe<sup>2+</sup>, Cu<sup>2+</sup>, Zn<sup>2+</sup>). Pristine and 4N-GQDs show comparable adsorption energies (−0.02 eV), while M-4N-GQDs exhibit stronger adsorption, ranging from −0.221 to −0.025 eV. Ti<sup>2+</sup>-4N-GQD achieves an optimal adsorption energy of −0.221 eV, making it highly suitable for hydrogen storage. The metal center’s charge transfer upon hydrogen adsorption influences binding strength. An external electric field (EEF) further reduces adsorption energy, promoting H<sub>2</sub> desorption. These results highlight Ti<sup>2+</sup>-4N-GQD’s potential for regulating H<sub>2</sub> adsorption and desorption in hydrogen storage applications.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115050"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanistic insights into the role of Glu103-mediated hydrogen bond shift in quercetin catalysis by Pirin homologs

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2024.115047

Chang Yuan , Guangju Chen , Hongwei Tan , Zongchao Jia

{"title":"Mechanistic insights into the role of Glu103-mediated hydrogen bond shift in quercetin catalysis by Pirin homologs","authors":"Chang Yuan , Guangju Chen , Hongwei Tan , Zongchao Jia","doi":"10.1016/j.comptc.2024.115047","DOIUrl":"10.1016/j.comptc.2024.115047","url":null,"abstract":"<div><div>YhhW and hPirin, as Pirin homologs, catalyze the conversion of quercetin to 2-protocatechuoyl-phloroglucinol carboxylic acid and CO. Compared to hPirin, YhhW exhibits lower catalytic efficiency in quercetin oxygenolysis and lacks C-terminal α-helix and Metal-Glu103 coordination. In this work, combined QM/MM calculations and MD simulations are utilized to investigate the detailed mechanisms of quercetin oxygenolysis by YhhW and hpirin. MD simulations reveal that the C-terminal helix in hPirin is crucial for stabilizing Metal-Glu103 coordination. QM/MM calculations further reveal that this coordination not only stabilizes the intermediate but also facilitates hydrogen bond shifts between Glu103 and the carbonyl group of quercetin, optimizing charge distribution and promoting the final ring formation. In contrast, the distal positioning of Glu103 in YhhW disrupts efficient hydrogen bond switching, leading to diminished activity. This work provides deeper insights into quercetin oxygenolysis mechanisms by Pirin homologs and sheds light on the role of hydrogen bond in enzymatic reactions.</div></div>","PeriodicalId":284,"journal":{"name":"Computational and Theoretical Chemistry","volume":"1244 ","pages":"Article 115047"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ReaxFF molecular dynamics investigation of hot spot under electric field in RDX embedded with carbon nanotube

IF 3 3区化学

Computational and Theoretical Chemistry Pub Date : 2025-02-01 DOI: 10.1016/j.comptc.2025.115083

Feng Miao , Lilai Wei , Min Xu , Xinlu Cheng , Zheng Wang , Shiquan Feng

引用次数: 0