Journal of Molecular Modeling最新文献

{"title":"Codoped germanene with 3p and 4p elements elements","authors":"Pablo A. Denis,&nbsp;Jose A. S. Laranjeira,&nbsp;Nicolas F. Martins,&nbsp;Julio R. Sambrano","doi":"10.1007/s00894-024-06133-6","DOIUrl":"10.1007/s00894-024-06133-6","url":null,"abstract":"<div><h3>Context</h3><p>The relentless need for new materials to be used in electronic devices has opened new research directions in materials science. One of them involves using two-dimensional materials, among which there is current interest in using germanene. The heteroatom doping of germanene has been proposed as a possible approach to fine-tuning its electronic properties. However, this procedure is complicated because locating the dopants with a specific arrangement is challenging, thus achieving reproducibility. To avoid this problem, we propose the codoping of germanene to understand if dopants prefer to be agglomerated as observed for graphene or if they prefer to adopt a random disposition. Herein, we employed first-principles calculations to study 21 codoped germanene systems with one <i>3p</i> (Al, Si, P, and S) and one <i>4p</i> (Ga, As, and Se) element. Our results indicate that in the cases of AlP, AlS, GaP, GaS, GaAs, and GaSe codoped germanene, the dopants show a tendency to be located in specific lattice positions. The ortho disposition of dopants is preferred for AlP, AlS, GaP and GaS codoped germanene and their <i>4p</i> counterparts GaAs and GaSe codoped germanene, and the materials showed interesting electronic properties making them suitable to develop germanene-based electronic materials.</p><h3>Methods</h3><p>We utilized the M06-L, HSE06 methods accompanied by the 6-31G* basis sets to perform periodic boundary conditions calculations as implemented in Gaussian 09. The unit cells were sampled employing 100 k-points for geometry optimizations and 2000 k-points for electronic properties The ultrafine grid was employed. Results were visualized employing Gaussview 5.0.1. In addition to this, we performed B3LYP-D3 periodic calculations as implemented in CRYSTAL17.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142204931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study on low-rank coal flotation collector screening and performance based on molecular polarity index","authors":"Lei Zhang,&nbsp;Shengyu Liu,&nbsp;Beilei Sun,&nbsp;Jianying Guo,&nbsp;Bao Li","doi":"10.1007/s00894-024-06129-2","DOIUrl":"10.1007/s00894-024-06129-2","url":null,"abstract":"<div><h3>Context</h3><p>Extensive studies using a trial-and-error approach have been conducted on low-rank coal flotation collectors. However, screening efficient collectors remains a considerable challenge due to the lack of suitable screening principles. It has proven that polar compounds such as carboxylic acids and esters are effective collectors for low-rank coal flotation. In this work, the effects of carboxylic acid, alcohol, and methyl ester on the floatability of low-rank coal were compared, the flotation performance of the polar collector was evaluated with theoretical calculations, a suitable evaluation parameter was determined and a screening principle based on this parameter was determined. The results show that the enhancement effects of polar collectors on low-rank coal floatability follow the order of methyl decanoate &gt; methyl laurate &gt; methyl octanoate &gt; sec-octanol &gt; methyl oleate (or methyl oleate &gt; sec-octanol) &gt; n-octanoic acid. Compared with the molecular polarity index, the hydrophobicity indices log P and dipole moment cannot be used to accurately evaluate different types of collectors and the same type of collectors, respectively. At room temperature, liquid polar compounds with molecular polarity indices in the range of 6.0 ~ 8.0 kcal/mol effectively enhance the floatability of low-rank coal. The molecular polarity index of the collector is used for the first time to screen effective collectors of low-rank coal in this work. This parameter is anticipated to be highly important for the development and research of low-rank coal and other mineral collectors.</p><h3>Methods</h3><p>To obtain reasonable and accurate molecular structure, geometry optimization and frequency calculations of the studied collectors were conducted via the Gaussian 09 software package based on density functional theory at the B3LYP/6–311 + G (d, p) level. The integral equation formalism for the polarizable continuum model (IEF-PCM) was utilized with water as the solvent (dielectric constant = 78.36, T = 298 K) for all the calculations. Then, the atomic charge distributions (MPA and NPA) and electrostatic potential maps, the dipole moment and molecular polarity index, and the log P and water solubilities of studied collectors were shown or calculated by Gauss View 5.0, Mutiwfn program and website (https://www.molsoft.com/mprop/mprop.cgi), respectively.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative computational analysis of orthoconic antiferroelectric liquid crystals: DFT analysis","authors":"Bharti Garg,&nbsp;Mohammad Shariq,&nbsp;Hussain J. Alathlawi,&nbsp;Eman Almutib,&nbsp;Tasneem H. Alshareef,&nbsp;Ali Alzahrani,&nbsp;Mohd Shakir Khan,&nbsp;Y. Slimani","doi":"10.1007/s00894-024-06127-4","DOIUrl":"10.1007/s00894-024-06127-4","url":null,"abstract":"<div><h3>Context</h3><p>The study undertakes a comparative analysis of four distinct semi-fluorinated chiral Organic Active Ferroelectric Liquid Crystals (OAFLCs). The comparative analysis of the compounds is done by using various parameters, including thermodynamic, non-linear optical, electrical, atomic charge distribution, and atomic orientations. We use optimization algorithms to look at chemical reactivity, electrical properties, intermolecular interactions, and static hyperpolarizability. Sample 4 is the best choice for a wide range of display applications. This research contributes to understanding the nuanced properties of semi-fluorinated chiral OAFLCs and highlights Sample 4’s potential for novel applications in display technology, owing to its superior stability and optimized properties. This study helps to enhance our understanding of the comparative analysis of semi-fluorinated chiral OAFLCs for potential advancements in display technologies by incorporating findings from key studies.</p><h3>Method</h3><p>The simulations are performed using density functional theory (DFT) with the B3LYP functional for predicting molecular properties, and Vibrational Energy Distribution Analysis (VEDA) software is used to perform the vibrational analysis of the molecules.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FEM simulation of SARS-CoV-2 sensing in single-layer graphene-based bionanosensors","authors":"Manisha Makwana","doi":"10.1007/s00894-024-06123-8","DOIUrl":"10.1007/s00894-024-06123-8","url":null,"abstract":"<div><h3>Context</h3><p>Airborne pathogens, defined as microscopic organisms, pose significant health risks and can potentially cause a variety of diseases. Given their ability to spread through diverse transmission routes from infected hosts, there is a critical need for accurate monitoring of these pathogens. This study aims to develop a sensor by investigating the vibrational responses of cantilever and bridged boundary-conditioned single-layer graphene (SLG) sheets with microorganisms, specifically SARS-CoV-2, attached at various positions on the sheet. The dynamic analysis of SLG with different boundary conditions and lengths was conducted using the atomistic finite element method (AFEM). Simulations were performed to evaluate SLG’s performance as a sensor for biological entities. Altering the sheet’s length and the mass of the attached biological object revealed observable frequency differences. This sensor design shows promise for enhancing the detection capabilities of graphene-based technologies for viruses.</p><h3>Methods</h3><p>Finite element method (FEM) analysis is employed to model the sensor’s performance and optimize its design parameters. The simulation results highlight the sensor’s potential for achieving high sensitivity and rapid detection of SARS-CoV-2. Bridged and cantilever boundary conditions are applied at the ends of the SLG structure by using ANSYS software. Simulations have been conducted to observe how SLG behaves when used as sensors. In armchair graphene, under both boundary conditions, an SLG (5, 5) structure with a length of 50 nm displayed the highest frequency when a SARS-CoV-2 molecule with a mass of 2.6594 × 10⁻¹⁸ g was attached. Conversely, the chiral SLG (17, 1) structure exhibited its lowest frequency at a length of 10 nm. This insight is crucial for grasping detection limits and how factors such as size and boundary conditions influence sensor efficacy. These biosensors hold immense promise in biological sciences and medical applications, revolutionizing patient care by enabling early detection and accurate pathogen identification in clinical settings.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical study on multi-perspective interaction analysis of ADN and ADN-H2O-CH3OH solutions","authors":"Li Tang,&nbsp;Lin-yan Wang,&nbsp;Jian-hui Han,&nbsp;Ji-fei Ye,&nbsp;Jun Yuan","doi":"10.1007/s00894-024-06130-9","DOIUrl":"10.1007/s00894-024-06130-9","url":null,"abstract":"<div><h3>Context</h3><p>Revealing the mechanism of intermolecular interactions in dinitroamine ammonium (ADN)-based liquid propellants and exploring the reasons for their performance changes, multi-perspective interaction analyses of ADN and ADN-water (H₂O)-methanol (CH₃OH) solutions have been conducted via theoretical methods. The band structure, density of states (DOS), surface electrostatic potential (ESP), Hirshfeld surface, reduced density gradient (RDG), AIM topological analysis, and detonation performance were studied and the results showed that both the ADN and ADN-H₂O-CH₃OH solutions had hydrogen bonds and van der Waals interactions. By introducing the small molecules H₂O and CH₃OH, the detonation performance of the ADN-H₂O-CH₃OH solution slightly decreased, but its sensitivity also decreased. Overall, the comprehensive performance of the ADN-H₂O-CH₃OH solution has improved, and the application range has expanded. These results are helpful for obtaining a deeper understanding of ADN-based liquid propellants at the atomic level and contribute to the development of new liquid propellants.</p><h3>Methods</h3><p>The ADN and ADN-H₂O-CH₃OH solutions were constructed by Amorphous cell module and optimized via GGA with PBE methods in the Dmol3 module of the Materials Studio, and their electronic properties were calculated. Hirshfeld surfaces were generated with CrystalExplorer 3.0. A topological analysis of a variety of molecular clusters was performed via QTAIM. The QTAIM and RDG analyses in this work were generated by Multiwfn 3.0.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The structural, electronic, optical, thermoelectric, and magnetic properties of the Perovskite PrFeO3: DFT and Monte Carlo simulations","authors":"S. Benyoussef,&nbsp;A. Jabar,&nbsp;S. Idrissi,&nbsp;N. Tahiri,&nbsp;L. Bahmad","doi":"10.1007/s00894-024-06122-9","DOIUrl":"10.1007/s00894-024-06122-9","url":null,"abstract":"<div><h3>Context</h3><p>Nowadays, Perovskite materials with diverse compositions and structures have garnered significant attention for their potential applications across various industrial and technological fields. Here, we investigated the structural, electronic, optical, thermodynamic, thermoelectric, and magnetic properties of perovskite PrFeO₃ using density functional theory and Monte Carlo simulations. The optimization results demonstrate that the ferromagnetic phase is more stable than the antiferromagnetic phase. Under the GGA + SOC + U and GGA + mBJ approaches, the electronic results of the PrFeO₃ compound expose the half-metallic and magnetic behavior. It was also demonstrated that introducing dilatation strain can effectively enhance both the mechanical and thermal stability of PrFeO₃. Additionally, the optical properties show that this material has potential uses for solar cells because of its capacity to absorb light in the ultraviolet (UV) spectrum. The maximum values of the Seebeck coefficient reach 90 µV/K at 1000 K, indicating the potential of PrFeO₃ as an efficient thermoelectric material. The magnetic properties exhibit a first transition of spin reorientation (<i>T</i>_SR) at 171.44 K, followed by a second-order transition at 707.15 K. This investigation provides valuable insights into the unstudied aspect of Perovskite PrFeO₃.</p><h3>Methods</h3><p>To carry out this investigation, we employed the density functional theory (DFT) implemented in the Wien2k package. To determine the exchange–correlation potential, we utilized the GGA-PBE (Perdew, Burke, and Ernzerhof) approach. The SOC was included based on the second-variational method using scalar relativistic wavefunctions, and electron–electron Coulomb interactions for Fe and Pr are considered in the rotationally invariant way GGA + SOC + U. In this paper, the effective parameter <i>U</i>_eff = <i>U</i> − <i>J</i> was adopted, where <i>U</i> and <i>J</i> stand for the Coulomb and exchange parameters, respectively. Also, we opted for the modified Becke–Johnson potential (mBJ) for comparison. The thermodynamic properties are obtained using the quasi-harmonic Debye model via Gibbs2 software programs. For the calculation of thermoelectric coefficients, a combination of first-principles band structure calculations and the Boltzmann transport theory within the rigid band approximation (RBA) and the constant scattering time approximation (CSTA) was employed, utilizing the BoltzTrap code. Subsequently, we delve into the magneto-caloric and magnetic properties by employing Monte Carlo simulations.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new dual-functional strategy to desensitize and sense the explosive and toxic 1,3,5-trinitro-1,3,5-triazinane by cyclo[n]carbons (n = 10,14,18)","authors":"Wei Chen,&nbsp;Qiong Wu,&nbsp;Wei Xu,&nbsp;Zusheng Hang,&nbsp;Weihua Zhu","doi":"10.1007/s00894-024-06125-6","DOIUrl":"10.1007/s00894-024-06125-6","url":null,"abstract":"<div><h3>Context</h3><p>In this work, in order to find new strategy to solve the safe problem of one famous high energy compound 1,3,5-trinitro-1,3,5-triazinane (RDX) under the impact and static electricity environment, cyclo[n]carbons (<i>n</i> = 10, C₁₀; <i>n</i> = 14, C₁₄; <i>n</i> = 18, C₁₈) were employed to construct novel energetic composites (RDX@C₁₀, RDX@C₁₄, RDX@C₁₈) with RDX for the first time. The investigated results showed that C₁₀, C₁₄ and C₁₈ all can form stable composites with RDX through a exothermal process. Three cyclo[n]carbons could not only decrease the impact sensitivity of RDX by decreasing the positive ESP values and transferring the HPV region. But also could reduce the electrostatic sensitivity greatly by decreasing the energy gap, increasing the <i>E</i>_HOMO and controlling the active electron-induced process and reaction. Among them, the desensitization effect by C₁₈ and C₁₄ was found to be much better than C₁₀. In addition, three cyclo[n]carbons may be used as new sensors for the detection of RDX, due to the fast recovery time under different lights, and great change in the UV–Vis spectrum. These improvements may provide valuable insights for enhancing the safe performance of high energy compounds with similar structures to RDX, and broaden the application sphere of cyclo[n]carbons.</p><h3>Methods</h3><p>All of the calculations on the structures were carried out by using the Gaussian 09 software at the M06-2X/6-311G(d,p) level. In addition, further calculations on the properties and interactions were performed by using the Multiwfn software.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GMXPolymer: a generated polymerization algorithm based on GROMACS","authors":"Jianchuan Liu,&nbsp;Haiyan Lin,&nbsp;Xun Li","doi":"10.1007/s00894-024-06119-4","DOIUrl":"10.1007/s00894-024-06119-4","url":null,"abstract":"<div><h3>Context</h3><p>This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used in this method are described in the main text, and example input scripts are provided for the GMXPolymer code, which is based on the GROMACS molecular dynamics package. To demonstrate the efficacy of our method, we apply it to different glassy polymers exhibiting varying degrees of functionality, polarity, and rigidity. The reliability of the method is validated by comparing simulation results with experimental data in various structural and thermal properties, both of which show excellent agreement.</p><h3>Methods</h3><p>This work implements the GMXPolymer simulated polymerization algorithm on the GROMACS program. GMXPolymer code controls the main polymerization loop. The energy minimizations and molecular dynamics simulations use the GROMACS program called by the GMXPolymer code. A new ITP file is generated when a new bond is formed, and the necessary additions to the ITP file are made to include new bonds, angles, and dihedrals. In preparing the ITP file of the monomer, the charge of the reactive atom must be modified before the code runs so that it is a correct value after bonding.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 9","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The origin of selectivity in the trimerization of 1,3-cyclopentadiene from an activation strain perspective","authors":"Ravshan S. Shamsiev,&nbsp;Nikolai A. Dontsenko","doi":"10.1007/s00894-024-06117-6","DOIUrl":"10.1007/s00894-024-06117-6","url":null,"abstract":"<div><h3>Context</h3><p>Quantum chemical modeling (DFT-PBE0/cc-pVTZ) of the [4 + 2]-cycloaddition reaction of 1,3-cyclopentadiene (CPD) to (exo/endo)-dicyclopentadiene (DCPD) was carried out, resulting in 14 products—CPD trimers. According to calculations, exo-addition of CPD to the norbornene (NB) fragment of DCPD and trans-addition of CPD to the cyclopentene (CP) fragment of DCPD are kinetically preferred. Ring strain energies <i>E</i>_RS were calculated for all trimers using the homodesmotic reaction approach. The least strained trimers are formed by exo-addition of CPD to the NB fragment of exo-DCPD, while the most strained ones are formed by endo-addition of CPD to the NB fragment of endo-DCPD. <i>E</i>_RS values are in good agreement with thermodynamic stability of trimers. Analysis of activation energy using the activation strain model showed steric effects causing deformation of the DCPD molecule upon reaching the transition state to be the leading factor of the magnitude of the cycloaddition reaction activation barrier. Deformation of the DCPD molecule mostly occurs in two dihedral angles—the angle of escape of H atoms from the plane of the double bond involved in cycloaddition and the angle between the NB and CP fragments. The sum of deviations of these angles in the transition states (or products) structures is in good agreement with Gibbs activation energies of cycloaddition reactions of CPD to DCPD.</p><h3>Methods</h3><p>Quantum chemical calculations were carried out using density functional theory in Gaussian 09 software. Hybrid exchange–correlation PBE0 functional was used with cc-pVTZ basis set.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical study of adsorption of gas (CO, CO2, NH3) by metal (Au, Ag, Cu)-doped single-layer WS2","authors":"Danqi Zhao,&nbsp;Yang Wen,&nbsp;Zhiqiang Li,&nbsp;Yan Cui,&nbsp;Yimin Zhao,&nbsp;Teng-Fei Lu,&nbsp;Ming He,&nbsp;Bo Song,&nbsp;Zhihua Zhang","doi":"10.1007/s00894-024-06118-5","DOIUrl":"10.1007/s00894-024-06118-5","url":null,"abstract":"<div><h3>Context</h3><p>The adsorptions of gas (CO, CO₂, NH₃) by metal (Au, Ag, Cu)-doped single layer WS₂ are studied by density functional theory. The doping of metal atoms makes WS₂ behave as n-type semiconductors. The final adsorption sites for CO, CO₂, and NH₃ are close to the atomic sites of the doped metal. The adsorptions of CO and NH₃ gases on Cu/WS₂, Ag/WS₂, and Au/WS₂ are dominated by chemisorption. The doped metal atoms enhance the hybridization of the substrate with the gas molecular orbitals, which contributes to the charge transfer and enhances the adsorption of the gas with the material surface. The adsorptions of CO and NH₃ on Cu/WS₂ and Ag/WS₂ allow favorable desorption in a short time after heating. The single-layer Cu/WS₂ is proved to have the potential to be used as a reliable recyclable sensor for CO. This work provides a theoretical basis for developing high-performance WS₂-based gas sensors.</p><h3>Methods</h3><p>In this paper, the adsorption energy, electronic structure, charge transfer, and recovery time of CO, CO₂, and NH₃ in the doped system have been investigated based on the CASTEP code of density functional theory. The exchange correlation function used is the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA). The TS (Tkatchenko-Scheffler) dispersion correction method was used to involve the effects of van der Waals interaction on the adsorption energies for all adsorption system. The ultrasoft pseudopotentials are chosen and the plane-wave cut-off energies are set to 500 eV. The k-point mesh generated by the Monkhorst package scheme is used to perform the numerical integration of the Brillouin zone and 5 × 5 × 1 k-point grid is used. The tolerances of total energy convergence, maximum ionic force, ionic displacement, and stress component are 1.0 × 10⁻⁵ eV/atom, 0.03 eV/Å, 0.001 Å, and 0.05 GPa, respectively.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"30 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}