Journal of Molecular Modeling最新文献

{"title":"Theoretical study of adsorption of gas (CO, CO₂, NH₃) by metal (Au, Ag, Cu)-doped single-layer WS₂.","authors":"Danqi Zhao, Yang Wen, Zhiqiang Li, Yan Cui, Yimin Zhao, Teng-Fei Lu, Ming He, Bo Song, Zhihua Zhang","doi":"10.1007/s00894-024-06118-5","DOIUrl":"https://doi.org/10.1007/s00894-024-06118-5","url":null,"abstract":"<p><strong>Context: </strong>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><p><strong>Methods: </strong>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>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"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}

{"title":"Structural, mechanical, electronic, vibrational properties and hydrogen bonding of a novel energetic ionic 5, 5'-dinitroamino-3, 3'-azo-oxadiazole 4, 7-diaminopyridazino [4, 5-c] furoxan salt.","authors":"Yu-Shi Liu, Wen-Shuo Yuan, Qi-Jun Liu, Fu-Sheng Liu, Zheng-Tang Liu","doi":"10.1007/s00894-024-06124-7","DOIUrl":"https://doi.org/10.1007/s00894-024-06124-7","url":null,"abstract":"<p><strong>Context and results: </strong>The structure, mechanical, electronic, vibration, and hydrogen bonding properties of a novel high-energy and low-sensitivity 5, 5'-dinitroamino-3, 3'-azo-oxadiazole 4, 7-diaminopyridazino [4, 5-c] furoxan salt have been studied by density functional theory. The calculated vibrational properties show that the low-frequency mode is mainly contributed by the vibration of the -NO2 group, and the high-frequency mode is mainly contributed by the vibration of the -NH2 group and the N7-H3 bond which protonates the cation. In addition, it is analyzed that the first bond to break may be the N-NO2 bond. The calculated hydrogen bond properties indicate that the hydrogen bond between water molecules and cations is N7-H3… O5 (1.563 Å), which is the shortest hydrogen bond among all hydrogen bonds. The presence of this exceptionally short hydrogen bond renders the N7-H3 and H6-O5 bonds resistant to disruption at high frequencies, underscoring the pivotal role of hydrogen bonding in stabilizing the structure of energetic materials. Given the absence of experimental and theoretical data on the electronic, mechanical, and vibrational properties of the material thus far, our calculations offer valuable theoretical insights into the ionic salts of high energy and low sensitivity.</p><p><strong>Computational methods: </strong>All calculations have been carried out based on density functional theory (DFT) and implemented in the CASTEP code. The mode-conserving pseudopotential is utilized to describe the plane wave expansion function, while the PBE functional within the generalized gradient approximation (GGA) is employed to characterize the exchange-correlation interaction. Additionally, dispersion correction is applied using Grimme's DFT-D method.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118721","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":"Advancing rational pesticide development against Drosophila suzukii: bioinformatics tools and applications-a systematic review.","authors":"Tarcisio Silva Melo, Bruno Silva Andrade","doi":"10.1007/s00894-024-06113-w","DOIUrl":"10.1007/s00894-024-06113-w","url":null,"abstract":"<p><strong>Context: </strong>Drosophila suzukii (Matsumura, 1931) is a widespread agricultural pest responsible for significant damage to various soft-skinned fruit hosts. The revolutionary potential of bioinformatics in agriculture emerges from its ability to provide extensive information on pests, fungi, chemical resistance, implications of non-target species, and other critical aspects. This wealth of information allows researchers to engage in projects and applied research in diverse agricultural domains that face these challenges. In this context, bioinformatics tools play a fundamental role. The negative impact of pests on crops, resulting in substantial economic losses, has highlighted the importance of in silico methods.</p><p><strong>Methods: </strong>To achieve this, we conducted a systematic search in scientific databases using as keywords \"Drosophila suzukii,\" \"biopesticides,\" \"simulations computational,\" and \"in-silico.\" After applying the filters of relevance and publication date, we organized the articles and prioritized those that directly addressed that matched the keywords and the use of bioinformatics tools. Additionally, we included studies focusing on in silico assays of biopesticides, such as molecular docking. Our review aimed to present a collection of recent literature on biopesticides against Drosophila suzukii, emphasizing bioinformatics methods. Through this work, we strive to contribute to the literature of new perspectives on the development and efficiency of biopesticides, along with to advance research that may improve pest control strategies.</p><p><strong>Results: </strong>In the results of the systematic review, we found 2734 articles related to the selected keywords. Six of these articles directly address Drosophila suzukii and the use of bioinformatics tools in the search for alternatives in pest control. In the selected studies, we observed that two articles tend to focus on phylogenetic approaches, searching for gene sequences, amino acids, and constructing phylogenetic trees. The other three articles used molecular modeling and docking of receptors such as GABA and TRP with plant-derived and synthetic compounds to study intermolecular interactions. However, we identified gaps in these studies that could lead to further research in the biorational development of biopesticides using bioinformatics tools.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103212","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":"High-throughput screening on optoelectronic properties of two-dimensional InN/GaN heterostructure from first principles.","authors":"Nitika, Sandeep Arora, Dharamvir Singh Ahlawat","doi":"10.1007/s00894-024-06121-w","DOIUrl":"https://doi.org/10.1007/s00894-024-06121-w","url":null,"abstract":"<p><strong>Context: </strong>A novel 2D InN/GaN lateral heterostructure (LHT) was simulated by stitching monolayer of 2D InN and monolayer of 2D GaN. The structural stability, electronic structure, and optical properties were systematically investigated using first-principle calculations and by considering the effects of strain. The results indicated that the designed heterostructure has a direct bandgap of 2.26 eV which is further affected by applied biaxial strain. The bandgap of 2D InN/GaN lateral heterostructure decreases with the increase in biaxial strain, and tensile strain triggers a direct-to-indirect energy gap changeover at + 6%. Additionally, under compressive strain, heterostructure remains a direct bandgap semiconductor. Furthermore, the strain significantly affects the optical characteristics of lateral heterostructure. It has been noticed that the first optical absorption peak moves from 2.51 eV (ɛ =  - 4%) to 1.40 eV (ɛ = 10%). Therefore, 2D InN/GaN lateral heterostructure provides an approachable way for utilizing in optoelectronic devices through the creation of in-plane lateral heterostructures.</p><p><strong>Methods: </strong>We performed all the computations using a self-consistent method based upon density functional theory. We used the PBEsol functional in the GGA to account for the exchange-correlation effects. We introduced a 10-Å vacuum region in the z-direction to avoid interaction between periodic images. We considered non-negligible weak dispersion correction in the lateral heterostructure using Grimme's DFT-D3 approach. In this study, we also computed the electrical and optical properties employing the local modified Becke-Johnson (lmBJ) exchange potential under meta-GGA functional to obtain more precise results.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103214","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":"First-principles study of the structure, electronic and optical properties of monolayer ZrX₃ (X = S, Se, Te).","authors":"Zhi-Yuan Qiu, Ya-Le Tao, Qi-Jun Liu, Zheng-Tang Liu","doi":"10.1007/s00894-024-06112-x","DOIUrl":"https://doi.org/10.1007/s00894-024-06112-x","url":null,"abstract":"<p><strong>Context and results: </strong>The structure, electronic and optical properties of single-layer transition metallic chalcogenides ZrX₃ (X = S, Se, Te) have been studied by density functional theory. The electron energy dispersion curve shows that ZrX₃ has semiconductor properties, in which the conduction band is mainly contributed by the correlated states of the Zr-d orbital, and the valence band is mainly contributed by the correlated states of the X-p orbital. It is found that b-axis and biaxial strain have great influence on the bandgap and the shift of density of states is also large. At the same time, the peak value of density of states increases greatly when biaxial strain is applied. It is of guiding significance for selecting suitable substrates to prepare two-dimensional ZrX₃ materials to study their electronic properties. The calculation of optical constants confirms that ZrX₃ has strong optical anisotropy. In the visible range, the light absorption efficiency of ZrX₃ in the direction of electric field polarization [100] is higher than that in the direction of [010]. The reflectance spectral results show that ZrS₃ and ZrSe₃ in the [100] directions have the highest reflectance, and ZrTe₃ in the [010] direction has the highest reflectance, even in the long electromagnetic radiation range (up to 10 eV), which is of great significance for the construction of visible optical devices.</p><p><strong>Computational method: </strong>All computations have been carried out based on density functional theory (DFT) as implemented in the CASTEP code. The pseudo-potential is adopted by the norm conserving, and the exchange correlation functional is adopted by the Perdew-Burke-Ernzerhof in local generalized gradient approximation (GGA).</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103213","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 modeling of electronic absorption spectra of ionized species of β-diketones.","authors":"Maxim A Lutoshkin","doi":"10.1007/s00894-024-06106-9","DOIUrl":"https://doi.org/10.1007/s00894-024-06106-9","url":null,"abstract":"<p><strong>Context: </strong>Direct DFT evaluation of negatively charged or highly π-delocalized systems is intrinsically problematic. Single ionized (anionic) forms of β-diketones combine both these issues. In this article, we have summarized and analyzed the experimental and theoretical spectral dataset for anionic forms of different substituted perfluorinated β-diketones that were obtained by our team during the past few years. Using previously collected experimental data, spectra of anion of diketones containing phenol, 2-furoyl, 2-thiophen, 2-selenophen, 2-tellorphe, 2-pyridin, 2-naphthyl, and N-methyl-pyrrole substituted rings were considered and chosen for the simulation. The X3LYP density functional demonstrates good results in both ultraviolet and visible parts of the diketones spectra. Minnesota family show predictable ability within the reasonable errors. The linear correlation between the Hartree-Fock exchange and the errors of estimation has been observed. Density functionals with a low contribution of HF weight (0-30%) provide better prediction accuracy.</p><p><strong>Methods: </strong>Quantum chemistry calculations were performed under eighteen density functionals (Slater, Becke, OPTX, LYP, PW91C, BPE0, B3LYP, CAM-B3LYP, X3LYP, TPSS, revTPSS, TPSSh, M06-L, M06, M06-2X, M06-HF, M11-L, MN15-L), paired with the SMD solvation model implemented in GAMESS US program package. Def2-SVP basis set functions were applied to light atoms, and CRENBL effective core potential was used to Tellurium.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046144","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":"Structural, electronic, and NLO properties of two acridone alkaloîds: DFT and TD-DFT studies.","authors":"Vincent de Paul Zoua, Albert Fouda Atangana, Atud Quiggle Asi, Ismaèl Figapka Pagoré, Simplice Joel Ndendoung Tatsimo, Rahman Abdoul Ntieche","doi":"10.1007/s00894-024-06114-9","DOIUrl":"https://doi.org/10.1007/s00894-024-06114-9","url":null,"abstract":"<p><strong>Context: </strong>The structural, electronic, and nonlinear optical properties of Verdoocridone A (Ver A) and B (Ver B) are examined theoretically in this study. The results showed that Ver A and B exhibit good electronic properties and can be used as new materials in NLO applications. According to their maximum absorption wavelength, Ver A (λ_max = 313 nm) enables production of vitamin D, while Ver B (λ_max = 319.55 nm) can help skin pigmentation.</p><p><strong>Methods: </strong>All calculations were performed at the DFT/B3LYP-D3/6-311 + G(d,p) level of theory using the Gaussian 16 software package. Excited states were simulated using the TD-DFT method at the CAM-B3LYP combined with 6-311 + (d,p) basis set. Also, the solvent effect was studied in water and benzene phases by the solvation model based on density (SMD) method.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015959","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":"Exploring the molecular solvatochromism, stability, reactivity, and non-linear optical response of resveratrol.","authors":"Igo T Lima, Ramon F C Gomes, Edson N C Paura, Patricio F Provasi, Rodrigo Gester, Antonio Rodrigues da Cunha","doi":"10.1007/s00894-024-06108-7","DOIUrl":"https://doi.org/10.1007/s00894-024-06108-7","url":null,"abstract":"<p><strong>Context: </strong>This work analyzes the isomerization effects and solvent contributions to the stability, electronic excitations, reactivity, and non-linear optical properties (NLO) of resveratrol molecules within the formalism of the Density Functional Theory. The findings suggest that resveratrol solvatochromism is significantly influenced by solvent polarization. The electronic and free energies (E and G) indicate that trans is the most stable conformer. The system is classified as a strong nucleophile. However, the analysis of the Fukui functions and the Mulliken charges indicate that cis-trans isomerization jointly affects the reactive indices of the carbon and hydrogen atoms. The results also suggest that solvent is relevant to solvatochromism and the NLO response. Both cis and trans conformers present strong <math><mrow><mi>π</mi> <mo>-</mo> <msup><mi>π</mi> <mo>∗</mo></msup> </mrow> </math> excitations that undergo a visible hypsochromic change when the polarity of the solvent increases. Once the absorption spectra are connected to the first hyperpolarization ( <math><mi>β</mi></math> ) by the Oudar and Chemla relation, the hypsochromism of resveratrol is the reason for the drop in the generation of the second harmonic when the ambient polarity decreases. The CAM-B3LYP DFT results suggest that resveratrol is interesting for NLO applications. Depending on the choice of solvent, values <math><mo>∼</mo></math> 50 times those observed for urea ( <math><mrow><mi>β</mi> <mo>=</mo> <mn>0.34</mn> <mo>×</mo> <msup><mn>10</mn> <mrow><mo>-</mo> <mn>34</mn></mrow> </msup> </mrow> </math> esu), which is a standard NLO material.</p><p><strong>Methods: </strong>The optimized geometries of cis and trans isomers of resveratrol in vacuum were obtained using Density Functional Theory (DFT) with the hybrid exchange-correlation function (CAM-B3LYP) and Pople basis set functions, specifically 6-311++G(d,p). The solvent effect on the geometries of both isomers was included using the polarizable continuum model (PCM) with the same level of QM calculation. Vibrational analysis was conducted to confirm that all optimized geometries correspond to the minimum energy. Various electronic properties, including dipole moments, molecular orbitals, transition energy, dipole polarizabilities, and global reactivity parameters, were calculated using both continuum and discrete solvation models based on the sequential QM/MM methodology. All QM calculations were performed with the Gaussian 09 program and the MC simulations with the DICE program. All NLO analysis was carried out using the Multiwfn code.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015958","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":"Computational study on the Maillard reactions of glucose and galactose with lysine.","authors":"Yuzhen Li, Yunqing Wang, Zhenmin Liu, Chunping You","doi":"10.1007/s00894-024-06105-w","DOIUrl":"https://doi.org/10.1007/s00894-024-06105-w","url":null,"abstract":"<p><strong>Context: </strong>Milk has nutrient-rich but thermal sensitive matrix that undergoes varying degrees of Maillard reaction (MR) at heating conditions. The MR mainly occurs between lysine residues (Lys) and lactose composed of glucose (Glc) and galactose (Gal), which are abundantly sourced from dairy products. In the present study, the MRs of Glc and Gal with Lys at the initial and intermediate stages have been investigated theoretically using density functional theory (DFT) to simulate the gaseous and aqueous phases. Reaction mechanisms have been proposed, and relative energy changes of different steps were calculated according to the total mass balance. The calculations reveal that both N^α- and N^ε-amine groups of Lys can react with the carbonyl functional group of Glc and Gal with the similar potential energy profiles, and Gal is more reactive than Glc. However, the barrier in N^ε-channel is lower than in N^α-channel, indicating a faster reaction rate through the former channel compared with the latter. The 5-hydroxymethyl-2-furfural (HMF) and derivative are formed under 3-deoxysone route in the intermediate stage. The calculation results are helpful for proposing a reasonable MR mechanism and suggesting possible control methods of the MRs.</p><p><strong>Methods: </strong>In this study, different levels of DFT calculations have been conducted to investigate the mechanisms and favorability of generating MR products in Glc-Lys and Gal-Lys models at initial and intermediate stages in the gaseous and aqueous conditions. In order to elucidate the molecular models from the perspectives of chemistry and geometry, DFT calculations were performed by the mean of B3LYP functional at basis sets of 6-311 +  + G (d, p) and 6-311 +  + G (2df, 2p) with optional solvation settings. To examine the solvation effect, the study further constructed models with solvent H₂O and calculated in wB97XD functional with 6-31 + G (d) basis set. All computations were carried out Gaussian 09 suite of quantum chemistry software.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003311","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 effect of strain effect on WS₂ monolayer as a potential delivery carrier for anti-myocardial infarction drug: First-principles study.","authors":"Xiao Zhu, Qinghua Yang, Yanmin Zhao, Xiusheng Sheng, Liangzhong Zhang","doi":"10.1007/s00894-024-06111-y","DOIUrl":"https://doi.org/10.1007/s00894-024-06111-y","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Context: &lt;/strong&gt;Myocardial infarction is one of the major health challenges. It is of great significance to develop potential delivery carriers for new anti-myocardial infarction drugs. In this paper, based on first-principles calculations, monolayer WS&lt;sub&gt;2&lt;/sub&gt; with excellent photoelectric properties was verified as a carrier for the anti-myocardial infarction drug amiodarone (AMD). Studies have shown that the WS&lt;sub&gt;2&lt;/sub&gt;-adsorbed AMD system (WS&lt;sub&gt;2&lt;/sub&gt;@AMD) maintains structural stability and produces an adsorption energy of-2.12 eV. Mulliken charge analysis shows that electrons are transferred from WS&lt;sub&gt;2&lt;/sub&gt; atoms to AMD atoms. Among them, C, N and O obtained the maximum values of 0.51,0.37 and 0.56 e electrons, respectively, while H and I lost the maximum values of 0.32 and 0.24 e electrons, respectively. The optical response of WS&lt;sub&gt;2&lt;/sub&gt; adsorbed AMD system is similar to that of WS&lt;sub&gt;2&lt;/sub&gt;. The light absorption coefficients of the two materials in the near ultraviolet region and the visible region can reach the order of 10&lt;sup&gt;5&lt;/sup&gt; cm&lt;sup&gt;-1&lt;/sup&gt; and 10&lt;sup&gt;4&lt;/sup&gt; cm&lt;sup&gt;-1&lt;/sup&gt;, and the strain makes the light absorption peak red-shifted. The feasibility of temperature-controlled release mechanism of WS&lt;sub&gt;2&lt;/sub&gt; as AMD carrier was discussed. This theoretical work helps to improve the performance of two-dimensional nanomaterials and make them better as drug delivery carriers to improve the therapeutic effect of myocardial infarction. These results indicate that the WS&lt;sub&gt;2&lt;/sub&gt; monolayer has potential applications in the development of drug delivery carriers.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;In this study, based on first-principles calculations, the CASTEP simulation software package was used to study the structure and properties of materials. The interaction between electrons and ions is considered by using Ultrasoft pseudopotentials. In order to eliminate the spurious interaction between adjacent structures caused by periodic calculations, a vacuum space no less than 18 Å is placed in the vertical direction if necessary. Different functions may produce different density functional calculation results. Due to the low sensitivity of the crystal structure to the calculation details, the PBE functional under the generalized gradient approximation (GGA) was initially used for structural optimization, and the energy cutoff value was set to 500 eV. Grimme 's dispersion correction was used to make the results more accurate. The Brillouin zone (BZ) is sampled by a 7 × 7 × 1 K-point grid to ensure the reliability of the original lattice calculation. The lattice vector and atomic coordinates are relaxed, and the tolerance of each atom is less than 0.01 eV/Å. The energy tolerance at the atomic position is less than 10&lt;sup&gt;-7&lt;/sup&gt; eV/atom. When calculating the band gap, the HSE06 hybrid functional is used to modify the optimized structure of the PBE functional to obtain more accurate results. Spin-polarized","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003312","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}