Journal of Molecular Modeling最新文献

{"title":"Thermophysical properties of graphene reinforced with polymethyl methacrylate nanoparticles for technological applications: a molecular model","authors":"Ernesto López-Chávez,&nbsp;Yesica A. Peña-Castañeda,&nbsp;Alberto Garcia-Quiroz,&nbsp;José A. I. Díaz Góngora,&nbsp;Fray de Landa Castillo-Alvarado","doi":"10.1007/s00894-024-06264-w","DOIUrl":"10.1007/s00894-024-06264-w","url":null,"abstract":"<div><h3>Context</h3><p>“Nanostructure of graphene-reinforced with polymethyl methacrylate” (PMMA-G), and vice versa, is investigated using its molecular structure, in the present work. The PMMA-G nanostructure was constructed by bonding PMMA with graphene nanosheet in a sense to get three different configurations. Each configuration consisted of polymeric structures with three degrees of polymerization (such as monomers, dimers, and trimers polymers, respectively). The results obtained make this new PMMA-G material more reliable and useful for several important technological applications, such as the construction of devices for hydrogen storage, batteries, super-capacitors, sensors and solar cells, and dental materials, among others. The PMMA reinforcement with graphene favors its thermal stability maintaining greater dimensional stability against thermal variations (minimal deformation); this is crucial for electronic devices and for packaging systems that undergo repeated thermal cycles during their manufacture, and also they are good thermal insulators. For microelectronic devices, such as chips and sensors, with low thermal expansion coefficients, it may prevent unwanted deformation. The PMMA density increases when it is reinforced with graphene, the polymers tend to be stiffer and stronger, important for applications where greater structural strength is required, and also become less soluble in solvents than pure PMMA and more resistant to the action of chemicals. Comparing a common polyvinyl chloride (PVC) material with the PMMA-G polymer, we found more advantages, such as the PMMA-G is less expensive, it has improved aesthetics, it is less rigid, it has more stable color, and it is less prone to keeping microorganisms alive, among others advantages.</p><h3>Methods</h3><p>Materials Studio (MS) software is used as the best and most reliable computational tool in the sense of analyzing some thermophysical properties of graphene reinforced with polymethyl methacrylate nanoparticles. The most stable PMMA nanostructures, graphene and PMMA-G, were obtained by applying density functional theory methods implemented by a DMol³ computational code under the MS software. The Synthia computational code, also under MS software, which is based on connectivity indices methods derived from graph theory combined with geometric variables, was also applied, to each polymerized structure, obtaining some of the important thermophysical properties; i.e., Van der Waals volume, molar volume, coefficient of volumetric thermal expansion, density, solid phase molar heat capacity at constant pressure, thermal conductivity, glass transition temperature, secondary relaxation temperature, and half decomposition temperature. The best-used hardware was a T7500 Dell Workstation, with 3.47 GHz Quad-Core Processors, 96 Gb RAM memory, and a perpetual MS software license.\u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995159","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":"Investigating the decomposition mechanism of DNAN/DNB cocrystal explosive under high temperature using ReaxFF/lg molecular dynamics simulations","authors":"Xin-yi Li,&nbsp;Bao-guo Wang,&nbsp;Ya-fang Chen,&nbsp;·Jian-sen Mao,&nbsp;·Ji-hang Du,&nbsp;Li Yang","doi":"10.1007/s00894-025-06281-3","DOIUrl":"10.1007/s00894-025-06281-3","url":null,"abstract":"<div><h3>Context</h3><p>DNAN/DNB cocrystals, as a newly developed type of energetic material, possess superior safety and thermal stability, making them a suitable alternative to traditional melt-cast explosives. Nonetheless, an exploration of the thermal degradation dynamics of the said cocrystal composite has heretofore remained uncharted. Consequently, we engaged the ReaxFF/lg force field modality to delve into the thermal dissociation processes of the DNAN/DNB cocrystal assembly across a spectrum of temperatures, encompassing 2500, 2750, 3000, 3250, and 3500 K. We analyzed the evolution of species, preliminary disintegration processes, and fluctuations in the quantification of terminal outcomes were examined. The findings suggest that 2,4-dinitroanisole (DNAN) undergoes a thorough phase of disassembly within a timespan of 218 ps, while 1,3-dinitrobenzene (DNB) completely decomposed within 228 ps, demonstrating that DNAN has lower thermal stability than DNB, but with no significant difference. The thermal dissociation of DNAN/DNB cocrystals at elevated temperatures reveals a triad of potential reaction sequences. Primordially, the denitration of DNAN transpires, succeeded by the denitration of DNB, culminating in the nitro-isomerization of the latter. This sequence implies that the nitro moieties within DNB possess inferior thermal resilience compared to their counterparts within the DNAN cocrystal matrix. An examination of the six resultant end products suggests a predominance of H2O, NO2, and H2 in comparison to the other byproducts, which may be indicative of the pyrolytic transformations occurring during the disassembly process.</p><h3>Methods</h3><p>This study first constructed the supercell model of DNAN/DNB eutectic crystal using the Materials Studio software and optimized the geometric structure of the model through the conjugate gradient algorithm. Then, the Nosé-Hoover method was used for NPT-MD simulation to further relax the model. Subsequently, molecular dynamics simulations were carried out using the LAMMPS software and the ReaxFF/lg force field. Simulation parameters were set, and NPT ensemble molecular dynamics simulations were performed at different temperatures. The simulation results were analyzed to reveal the thermal decomposition mechanism of DNAN/DNB eutectic crystal.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995158","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 influence of temperature and pressure on the self-diffusion characteristics and mechanical sensitivity of DNTF: a molecular dynamics study","authors":"Chen Li,&nbsp;Biao He,&nbsp;Jingyan Wang,&nbsp;Yaning Li,&nbsp;Linjing Tang,&nbsp;Zhiwei Han","doi":"10.1007/s00894-024-06269-5","DOIUrl":"10.1007/s00894-024-06269-5","url":null,"abstract":"<div><h3>Context</h3><p>3,4-Bis(3-nitrofurazan-4-yl) furoxan (DNTF) is a typical low-melting-point, high-energy–density compound that can serve as a cast carrier explosive. Therefore, understanding the safety of DNTF under different casting processes is of great significance for its efficient application. This study employed molecular dynamics simulations to investigate the effects of temperature and pressure on the self-diffusion characteristics and mechanical sensitivity of DNTF. The analysis focused on the mean square displacement, self-diffusion coefficient, cohesive energy density, non-bonded energy, and critical bond length of DNTF under various temperatures (250 to 450 K) and pressures (0.1 to 10 MPa). The results indicate that the self-diffusion coefficient and mechanical sensitivity of DNTF are more sensitive to changes in temperature. As the temperature increases, the self-diffusion behavior of DNTF accelerates, making it more volatile. This effect is particularly notable within the temperature range of 350 to 400 K, where the growth rate of the self-diffusion coefficient is significantly faster than in the 250 to 350 K range. The trigger bond length (<i>L</i>_<i>max</i>) gradually increases with rising temperature, accurately reflecting the objective trend that mechanical sensitivity increases with temperature. The results of this study provide a theoretical basis for the application of DNTF in high-energy materials, particularly in enhancing its safety.</p><h3>Methods</h3><p>An 8 × 4 × 2 supercell model comprising 256 DNTF molecules was constructed in the Materials Studio 8.0 package. The DNTF supercell was geometrically relaxed using the conjugate gradient method. Subsequently, a 10-ps NPT molecular dynamics simulation was conducted on the supercell under conditions of 300 K and 0.1 MPa to relieve internal stresses, thereby obtaining DNTF crystals in the equilibrium state. NPT molecular dynamics simulations of the DNTF supercell were then carried out under the COMPASS force field at constant temperature. The temperatures were set to 250 K, 300 K, 350 K, 400 K, and 450 K, and the pressures were set to 0.1 MPa, 1 MPa, 3 MPa, 5 MPa, and 10 MPa. The total simulation time was 1000 ps with a time step of 1 fs. Every 1000 steps, information on mean square displacement, non-bonded energy, intermolecular forces, and critical bond length was recorded.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995055","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":"Density functional theory study of hydrogen and oxygen reactions on NiO(100) and Ce doped NiO(100)","authors":"Bingxing Yang,&nbsp;Rong Zhang,&nbsp;Yunjie Sun","doi":"10.1007/s00894-024-06275-7","DOIUrl":"10.1007/s00894-024-06275-7","url":null,"abstract":"<div><h3>Context</h3><p>This study aims to reveal the reaction mechanisms of H₂ and O₂ on the NiO(100) and Ce-doped NiO(100) surfaces using the density functional theory (DFT) combined with the on-site Coulomb correction (DFT + U) method. It was found that H₂ and O₂ react favorably on the reduced surfaces of both materials. However, after the oxygen vacancy is filled, the activation energy for the reaction between H₂ and lattice oxygen increases. Ce doping reduces this activation energy to 1.64 eV (compared to 3.16 eV for pure NiO(100)). The enhanced activity of lattice oxygen due to Ce doping is attributed to the charge transfer in the Ce–O bond, which leads to the electronic localization around O atoms and weakens the activation energy barrier. Moreover, the presence of Ce facilitates the formation of a sub-stable OH intermediate on the reduced surface, ensuring the sustainability of the reaction. This study provides a theoretical basis for the design of high-performance nickel-based hydrogen deoxidizers and contributes to promoting the research and development process of nickel-based catalysts in related fields.</p><h3>Methods</h3><p>The calculations were performed using the Vienna ab initio simulation package (VASP) module of the MedeA® software. The exchange–correlation energy calculations are performed using the Perdew, Burke and Ernzerhof (PBE) functional within the generalized gradient approximation (GGA). The transition states were calculated using the MedeA® Transition State Search Module, based on the climbing-image nudged elastic band (CI-NEB) method.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976648","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 comprehensive study of the influence of non-covalent interactions on electron density redistribution during the reaction between acetic acid and methylamine","authors":"Olivier Aroule,&nbsp;Emilie-Laure Zins","doi":"10.1007/s00894-024-06249-9","DOIUrl":"10.1007/s00894-024-06249-9","url":null,"abstract":"<div><h3>Context</h3><p>A chemical reaction can be described, from a physicochemical perspective, as a redistribution of electron density. Additionally, non-covalent interactions locally modify the electron density distribution. This study aims to characterize the modification of reactivity caused by the presence of non-covalent interactions such as hydrogen bonds, in a reaction involving the formation of two bonds and the breaking of two others: CH₃COOH + NH₂CH₃ → CH₃CONHCH₃.</p><h3>Methods</h3><p>In this work, we will follow the how a reaction mechanism involving the formation of two chemical bonds and the breaking of two other chemical bonds is affected by non-covalent interaction. To this end, the reaction force will be used to define the region of the reagents, the region of the transition state, and the region of the products. We will analyze the redistributions of electron density and electron pairs in each of the regions of the reaction mechanisms, using QTAIM and ELF, topological analyses, respectively, for the reaction between methylamine and acetic acid, in the presence of 0 to 4 water molecules. DFT calculations were carried out at the LC-ωPBE/6–311 + + G(d,p) + GD3BJ level along the intrinsic reaction coordinate of the one-step reaction leading to the formation of methylacetamide.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976408","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":"Molecular dynamic simulation study on the influence of heating rate on the thermal decomposition process of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)","authors":"Xianfeng Wei,&nbsp;Shan Sha,&nbsp;Qingying Duan","doi":"10.1007/s00894-024-06270-y","DOIUrl":"10.1007/s00894-024-06270-y","url":null,"abstract":"<p>To clarify the effect of heating rate on the thermal decomposition process of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), this study employs molecular dynamic simulations to investigate the thermal decomposition of TATB at heating rates of 20, 40, 60, and 80 K/ps. The initial temperature is uniformly set to 300 K, while the final temperature is set to 3000 K. Results indicate that within the temperature range of 300–3000 K, the thermal decomposition rate of TATB decreases with increasing heating rate, whereas the initial decomposition temperature of TATB increases, consistent with the experimental pattern. Within the studied temperature range, a lower heating rate results in a higher number of decomposition fragments, leading to more effective collision between active fragments, facilitating more effective collisions between active species, and leading to the formation of more stable products such as H₂O, CO₂, and N₂. Conversely, higher heating rates reduce the quantities of these stable products. This study enhances the understanding of TATB’s thermal decomposition mechanism, providing valuable insights for its safe handling and application.</p><p>The Gaussian09 software was used to calculate the BDEs of TATB molecules, while the MD simulation using the ReaxFF-lg force field was performed by the LAMMPS package. Visualization and postprocessing were conducted using the OVITO software, and a custom script was developed to analyze the reaction products and frequencies.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976631","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":"Correction to: Constructing, in silico, molecular self‑aggregates and micro‑hydrated complexes of oxirene and thiirene","authors":"Dipali N. Lande,&nbsp;Shridhar P. Gejji,&nbsp;Rajeev K. Pathak","doi":"10.1007/s00894-025-06280-4","DOIUrl":"10.1007/s00894-025-06280-4","url":null,"abstract":"","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963188","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 the modulation mechanism of the optoelectronic properties based on common electrode metal atom adsorption on graphene/MoTe2","authors":"Jiabin Li,&nbsp;Nan Yang,&nbsp;Zenghui Fan,&nbsp;Jiang Wang,&nbsp;Yinghang Lei","doi":"10.1007/s00894-024-06268-6","DOIUrl":"10.1007/s00894-024-06268-6","url":null,"abstract":"<div><h3>Context</h3><p>The two-dimensional graphene/MoTe₂ heterostructure holds extensive potential applications in optoelectronic devices, sensors, and catalysts. To expand its optical applications, this study systematically investigates the adsorption stability of metal atoms (Au, Pt, Pd, and Fe) on the graphene/MoTe₂ and their influence on its optoelectronic properties employing first-principles methods. The findings indicate that after the adsorption of Au and Pd, the structure retains its direct bandgap properties, while the adsorption of Pt and Fe exhibits indirect bandgap characteristics. The work functions for all adsorbed structures are lower compared to the pristine graphene/MoTe₂. The total density of states is primarily derived from the C-2p, Mo-4d, Te-5p orbitals, as well as the <i>d</i> and <i>s</i> orbitals of the adsorbed atoms. The pristine graphene/MoTe₂ exhibits significant absorption in the ultraviolet range. Once graphene/MoTe₂ is adsorbed by metal atoms, it can significantly enhance the optical absorption across the spectrum from infrared to ultraviolet light. These findings provide important theoretical guidance for regulating the application of graphene/MoTe₂ in optoelectronics and related fields.</p><h3>Methods</h3><p>All analyses are grounded in density functional theory first principles and computed using CASTEP. Graphene/MoTe₂ consists of 4 × 4 × 1 single-layer, graphene single layer, and 3 × 3 × 1 single-layer MoTe₂. To prevent interactions between neighboring unit cells, a 20 Å vacuum space in the <i>z</i>-direction is employed. The electronic exchange–correlation interactions are treated using the Perdew-Burke-Ernzerhof functional within the framework of the generalized gradient approximation. Van der Waals (vdW) interactions are incorporated using the vdW correction function proposed by Grimme, which effectively describes vdW interactions. During the simulation, the cutoff energy for plane wave expansion is set to 420 eV, and the k-point grid is set to 4 × 4 × 1. The atomic displacement convergence standard is 0.002 Å, the internal stress convergence standard is 0.1GPa, and the interaction force convergence standard between atoms is 0.05 eV/Å. The convergence threshold for the iteration precision is set to ensure that the total energy for each atom is not less than 2 × 10⁻⁵ eV/atom.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963186","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":"Towards a unified fold-cusp model for bond polarity scaling: electron rearrangements in the pyrolytic isomerization of cubane to cyclooctatetraene","authors":"Leandro Ayarde-Henríquez,&nbsp;Cristian Guerra,&nbsp;Patricia Pérez,&nbsp;Eduardo Chamorro","doi":"10.1007/s00894-024-06229-z","DOIUrl":"10.1007/s00894-024-06229-z","url":null,"abstract":"<div><h3>Context</h3><p>This study meticulously examines the criteria for assigning electron rearrangements along the intrinsic reaction coordinate (IRC) leading to bond formation and breaking processes during the pyrolytic isomerization of cubane (CUB) to 1,3,5,7-cyclooctatetraene (COT) from both thermochemical and bonding perspectives. Notably, no cusp-type function was detected in the initial thermal conversion step of CUB to bicyclo[4.2.0]octa-2,4,7-triene (BOT). Contrary to previous reports, all relevant fluxes of the pairing density must be described in terms of fold unfolding. The transannular ring opening in the second step highlights characteristics indicative of a cusp-type catastrophe, facilitating a direct comparison with fold features. This fact underscores the critical role of density symmetry persistence near topographical events in determining the type of bifurcation. A fold-cusp unified model for scaling the polarity of chemical bonds is proposed, integrating ubiquitous reaction classes such as isomerization, bimolecular nucleophilic substitution, and cycloaddition. The analysis reveals that bond polarity index (BPI) values within the [0, 10⁻⁵] au interval correlate with cusp unfolding, whereas fold spans over a broader [10⁻³, ∞) au spectrum. These insights emphasize that the cusp polynomial is suitable for describing chemical processes involving symmetric electron density distributions, particularly those involving homolytic bond cleavages; in contrast, fold characterizes most chemical events.</p><h3>Methods</h3><p>Geometry optimization and frequency calculations were conducted using various DFT functionals. In line with recent findings concerning the rigorous application of BET, the characterization of bond formations and scissions via unfoldings was carried out by carefully monitoring the determinant of the Hessian matrix at all potentially degenerate CPs and their relative distance. The computed gas-phase activation enthalpies strongly align with experimental values, stressing the adequacy of the chosen levels of theory in describing the ELF topography along the IRC. The BPI was determined using the methodology proposed by Allen and collaborators.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963185","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":"Molecular structure characteristic of coals of different rank","authors":"Xiulin Shang,&nbsp;Zhongqi Wei,&nbsp;Di Tang,&nbsp;Zhijun Zhang","doi":"10.1007/s00894-024-06272-w","DOIUrl":"10.1007/s00894-024-06272-w","url":null,"abstract":"<div><h3>Context</h3><p>Understanding the structural characteristics of coal at the molecular level is fundamental for its effective utilization. To explore the molecular structure characteristic, the long-flame coal from Daliuta (DLT), coking coal from Yaoqiao (YQ), and anthracite from Taixi (TX) were investigated using various techniques such as elemental analysis, Fourier transform infrared spectroscopy, solid-state ¹³C nuclear magnetic resonance spectroscopy, and X-ray photoelectron spectroscopy. Based on the structural parameters, the coal molecular model was constructed and optimized. The molecular formula of DLT was C₁₉₃H₁₇₈N₂O₄₇, that of YQ was C₂₀₁H₁₇₉N₃O₃₀S, and that of TX was C₁₉₈H₁₁₈N₂O₁₀. With an increase in the degree of metamorphism, the substitution of the benzene ring gradually shifted towards lower levels of substitution. The content of long chain in the aliphatic chain decreased while the content of branched chains kept increasing. The percentage of aromatic ether increased gradually, while the phenolic hydroxyl group initially decreased but then increased. The carboxyl group C = O decreased and eventually disappeared in anthracite coal. The proportion of pyrrole nitrogen gradually increased while that of pyridine nitrogen and protonated pyridine gradually decreased.</p><h3>Methods</h3><p>The 2D planar structure of coal was constructed using ChemDraw, ACD/CNMR Predictor, and gNMR programs. The geometry optimization was performed using the COMPASS II force field within the Forcite module in Materials Studio 2020. The annealing process employed NVT ensemble at a simulation temperature of 298 K. The Amorphous Cell module in Materials Studio was used to construct large-scale 3D molecular models, with the set parameters in this paper.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963187","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}