Journal of Molecular Modeling最新文献

{"title":"Density functional theory for nanomaterials: structural and spectroscopic applications-a review.","authors":"Ansa Latif, Anam Latif, Muhammad Mohsin, Ijaz Ahmad Bhatti","doi":"10.1007/s00894-025-06431-7","DOIUrl":"https://doi.org/10.1007/s00894-025-06431-7","url":null,"abstract":"<p><strong>Context: </strong>Nanoparticles (NPs) exhibit unique physical and chemical properties that defy classical mechanics, owing to their quantum nature. These properties are dictated by size, shape, and structure, rendering NPs indispensable across diverse applications, including catalysis, medical imaging, drug delivery, and energy research. Advanced computational tools have become indispensable in unraveling the intricacies of nanomaterial behavior, driving significant progress in theoretical and computational research. Among these tools, the density functional theory (DFT) has emerged as a powerful method for predicting material properties. In this review study, we delve into key aspects of DFT simulations applied to nanomaterials, including Optimal Geometries, Band Gap and Electronic Properties, Density of States (DOS), Natural Bond Orbitals (NBO), and spectroscopic features (Infrared, Raman Spectra, and UV-Visible Spectra). Despite its successes, DFT faces limitations, particularly concerning semiconductor materials. Researchers strive to enhance its accuracy while maintaining computational efficiency. Balancing generically accurate functionals for specific applications remains an ongoing challenge. As nanomaterial continues to play a significant part in a variety of industries, the progress of DFT is of great interest and exploration.</p><p><strong>Methods: </strong>This review discusses DFT-based computational techniques employed for modeling nanomaterials. The calculations are generally done by utilizing generalized gradient approximation (GGA) functionals such as PBE (Perdew-Burke-Ernzerhof), and where necessary, hybrid functionals like B3LYP to enhance band gap accuracy. All calculations are performed using the standard quantum chemistry packages such as VASP, Gaussian, or Quantum ESPRESSO. This combination of methods offers a complete theoretical basis for the study of nanomaterial properties.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"211"},"PeriodicalIF":2.1,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666807","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 interactions of Cr₂O_n and Mn₂O_n clusters with H₂ molecules.","authors":"Konstantin V Bozhenko, Andrey N Utenyshev, Lavrenty G Gutsev, Sergey M Aldoshin, Gennady L Gutsev","doi":"10.1007/s00894-025-06437-1","DOIUrl":"https://doi.org/10.1007/s00894-025-06437-1","url":null,"abstract":"<p><strong>Context: </strong>Gas sensors with high sensitivity and selectivity are essential for industrial safety and environmental monitoring. The ongoing development of more effective sensors relies on two key aspects: the design of novel sensing materials and a deeper understanding of the underlying sensing mechanisms. Among the various materials used for the sensor fabrication, semiconducting metal oxides such as chromium and manganese oxides have garnered much recent attention. Notably, palladium-doped chromium oxide has demonstrated high efficiency in hydrogen sensing. Chromium oxides can function as single-component sensors and also in components of composite systems. Manganese oxides are likewise widely used in sensing applications, especially as electrochemical sensors either alone or in combination with other metal oxides.</p><p><strong>Methods: </strong>All calculations were carried out by using spin-polarized density functional theory with the generalized gradient approximation as implemented in Gaussian 09. Among the numerous exchange-correlation functionals and basis sets, we chose the BPW91 functional and 6-311 + G* basis set of triple-zeta quality. We considered reactions of Cr₂O_n and Mn₂O_n with H₂ and found pathways leading from the reagents to products. All but one reaction pathways were found to have two or three transition states separated by local minima. The search of transition states was performed by using the modified conjugate gradient algorithm and the local minima were determined by applying the intrinsic reaction coordinate algorithm. It was found that some of the pathways are spin-dependent, i.e., the total spin magnetic moments of reagents do not match those of the products.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"213"},"PeriodicalIF":2.1,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666809","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":"Microhydration of phenylboronic acid and its hydration free energy.","authors":"Doungous Sale, Alhadji Malloum, Mama Nsangou, Jean Jules Fifen, Jeanet Conradie","doi":"10.1007/s00894-025-06436-2","DOIUrl":"10.1007/s00894-025-06436-2","url":null,"abstract":"<p><strong>Context: </strong>Understanding the interactions of phenylboronic acid with its surrounding water molecules is essential for several applications in solvated systems. In the present work, we investigated the microhydration of the phenylboronic acid (PBA) and calculated its hydration free energy using the cluster continuum solvation model. Microhydration of PBA has not been investigated previously in the literature. It requires the structures of PBA to be surrounded by n explicit water molecules (PBA-W <math><mmultiscripts><mrow></mrow> <mi>n</mi> <mrow></mrow></mmultiscripts> </math> ). The results show that the B(OH) <math><mmultiscripts><mrow></mrow> <mn>2</mn> <mrow></mrow></mmultiscripts> </math> unit of phenylboronic acid forms clusters with water molecules that are similar to those of neutral water clusters. The QTAIM analysis shows that the structures of phenylboronic acid-water clusters are stabilized by strong OH <math><mo>⋯</mo></math> O and weak CH <math><mo>⋯</mo></math> O hydrogen bonds. In addition to QTAIM analysis, NBO analysis was also performed on the most stable configurations to better understand the delocalization of electron density from donor to proper acceptor within the compound. In addition, we found that the most stable structures dominate the population of the clusters for temperatures from 20 to 400 K. Finally, using the structures of the microhydrated phenylboronic acid, we estimated the free energy of hydration and the enthalpy of hydration of PBA. At room temperature, the phenylboronic acid's free energy and enthalpy of hydration are respectively evaluated to be <math><mo>-</mo></math> 72.1 kcal/mol and <math><mo>-</mo></math> 85.5k cal/mol. Assessment of temperature effects on the free energy and the enthalpy of hydration shows that the enthalpy is temperature-independent, while the free energy increases linearly with temperature.</p><p><strong>Methods: </strong>Initial configurations of PBA-W <math><mmultiscripts><mrow></mrow> <mi>n</mi> <mrow></mrow></mmultiscripts> </math> have been generated using classical molecular dynamics and subsequently optimized using the level of theory, <math><mi>ω</mi></math> B97X-D/def2-TZVP. Optimizations, frequency calculations, and NBO analysis are performed using the Gaussian 16 suite of programs. On the most stable configurations, we have performed the quantum theory of atoms in molecules (QTAIM) analysis to get insights into the hydrogen bond network of PBA-W <math><mmultiscripts><mrow></mrow> <mi>n</mi> <mrow></mrow></mmultiscripts> </math> . QTAIM is performed using AIMAll software. Thermodynamic properties as a function of temperature are evaluated using a homemade FORTRAN code-named TEMPO.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"212"},"PeriodicalIF":2.1,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential use of deep eutectic solvents based on sugar as green separation media for the acidic gases capture process from the gas mixtures: molecular dynamics simulation and COSMO-RS insights.","authors":"Samaneh Barani Pour, Nasrin Jabbarvand Behrooz, Jaber Jahanbin Sardroodi, Mohammad Sadegh Avestan","doi":"10.1007/s00894-025-06430-8","DOIUrl":"https://doi.org/10.1007/s00894-025-06430-8","url":null,"abstract":"<p><strong>Context: </strong>The global greenhouse gas (GHG) emissions originate from five main economic sectors: energy, industry, construction, transportation, and AFOLU (agriculture, forestry, and other land uses). The emissions of these gases from fossil fuels and land use have reached their highest levels since the nineteenth century. Consequently, urgent actions are required to address this issue worldwide to deal with specific challenges affecting air quality and weather conditions. For this purpose, the reduction of environmental pollutants requires finding methods, including extraction techniques using green solvents (DESs). Understanding the interactions between acid gases (H₂S/CO₂) and the eutectic solvent components (HBA/HBD) determines how much pollutant is absorbed by deep eutectic solvents (DESs). In this regard, to better comprehend the mechanism of H₂S gas absorption, we calculated the combined distribution functions (CDFs) involving the radial distribution functions (RDFs) and the angular distribution functions (ADFs). Additionally, we examined the hydrogen-bonding network, density profiles, spatial distribution functions (SDFs), and the nonbonded energies between H₂S and DES (choline chloride (ChCl)-glucose (Glu)/fructose (Fru) with a molar ratio of 2:1) components were calculated at 333 K. Furthermore, at the pressure between 1 and 15 atm, we obtained the solubility of H₂S/CO₂ gases, solubility selectivity, and diffusivity selectivity parameters as pressure functions to assess the efficacy of sugar-based DES in natural gas sweetening procedures. By analyzing how the interaction of H₂S molecules with the DES components, we concluded that the eutectic solvents based on glucose (Glu)/fructose (Fru) and choline chloride (ChCl) can absorb H₂S molecules.</p><p><strong>Methods: </strong>The molecular graphics program VMD and the PACKMOL package have been used to prepare DES components and simulation boxes. First, initial configurations were minimized under the periodic boundary condition, and then the systems were heated to T = 333 K. Then, a 50 ns NPT simulation was performed at 333 K, while gradually decreasing the distance between the two boxes until reaching equilibrium. The conductor-like screening model (COSMO), as a novel method, has been utilized to predict some properties. The TURBOMOLE program package has been employed to determine the geometries of the electronic density of each HBA and HBD in targeted deep eutectic solvents (optimizing the geometry of DESs components with Becke-Perdew-86 (BP86) functional along with a triple zeta valence potential (TZVP) basis set).</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"210"},"PeriodicalIF":2.1,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625238","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":"How does the conformational landscape change on replacement in tetralin? A computational investigation with oxygen, sulfur, and selenium.","authors":"Asif Iqubal Middya, Abhijit Chakraborty","doi":"10.1007/s00894-025-06432-6","DOIUrl":"https://doi.org/10.1007/s00894-025-06432-6","url":null,"abstract":"<p><strong>Context: </strong>The oxygen, sulfur, and selenium derivatives of tetralin termed as isochroman (IC), isothiochroman (ITC), and isoselenochroman (ISC) showed interesting conformational patterns. In particular, ITC and IC have immense pharmacological significance. The twisted conformer is the global minimum in IC, where the bent is a transition state (TS) and remains 1100 ± 100 cm^-1 higher. The bent form in ITC and ISC possesses the lowest energy. But, the twisted conformer lies higher by about 80 ± 20 cm^-1 in ITC and 700 ± 50 cm^-1 in ISC. The potential energy surfaces (PES) locate all the conformations and TSs. Molecular electrostatic potentials indicate the sites of electrophilic interactions, and the small energy difference between the minima in ITC predicts an interesting interplay of intermolecular interactions in suitable environments. The validity of the maximum hardness principle and minimum electrophilicity principles is checked. Frontier molecular orbitals show the change in electron densities on excitation, which are mostly π → π^* in nature. Hyperconjugative interactions involving different σ and lone pair orbitals explain the change in conformational patterns in these molecules. We suggest some experiments to corroborate our findings.</p><p><strong>Methods: </strong>Computations are performed with different functionals (B3LYP, M06-2X, and ωB97X-D) in DFT as well as ab initio methods (MP2 and CCSD) with 6-311G +  + (2d, 3p) and augmented cc-pVDZ as basis sets. Gaussian 09 is used for the above computations. PED analyses were performed by Veda 4 software. For viewing and plotting purposes, Gaussview 5.0 and Origin 8.5 are used.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"207"},"PeriodicalIF":2.1,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615703","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":"Screening of ionic liquids as sustainable catalyst for production of n-butyl acetate using COSMO-RS model.","authors":"Anantharaj Ramalingam, Achsah Rajendran Startha Christabel, Gayathri Mahavishnu","doi":"10.1007/s00894-025-06434-4","DOIUrl":"https://doi.org/10.1007/s00894-025-06434-4","url":null,"abstract":"<p><strong>Context: </strong>A total of 42 cations and 32 anions resulting in 1344 possible combinations were screened for green esterification process via the conductor-like screening model for real solvents (COSMO-RS model). The esterification reactants and products; n-butanol (n-BuOH), acetic acid (HAc), and n-butyl acetate (n-BuAc) in different combination of cation and anions were used to predict the activity coefficient at infinite dilution (IDAC) with the help of screening charge density. From the predicted IDAC values, the selectivity (S), capacity (C), and performance index (PI) were calculated to screen potential ionic liquids (ILs) for the green esterification process. Further, the σ-profile, and σ-potential of ILs, reactants, and products were generated and analysed.</p><p><strong>Methods: </strong>Molden Visualization Software, Gaussian 03 software, COSMOthermX (Version:19.0.5) were used to predict IDAC, sigma profile, and sigma potential. Hartree-Fock level and basis set 6-31G*. Density functional theory (DFT) with PBVP86 in combination with the basis set SVP (split valence polarised) and the density fitting basis set DGA1 (density gradient approximation)-#P BVP86/SVP/DGA1.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"208"},"PeriodicalIF":2.1,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615705","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":"Separation mechanism and chiral-HPLC chromatogram profile of racemic mandelate compounds: a comparative study between experiment and computation using conformer-rotamer ensemble sampling tool (CREST)-XTB.","authors":"Fenti Fatmawati, Aditya Wibawa Sakti, Suci Zulaikha Hildayani, Akhmaloka, Fida Madayanti Warganegara, Muhamad Abdulkadir Martoprawiro","doi":"10.1007/s00894-025-06408-6","DOIUrl":"https://doi.org/10.1007/s00894-025-06408-6","url":null,"abstract":"<p><strong>Context: </strong>Nearly 90% of drugs on the market are racemates. A racemate is a mixture of two enantiomers or substances in equal amounts that have an asymmetric molecular structure that is a mirror image of each other. Despite having the same chemical structure, chiral drug isomers can exhibit very different biological behaviors in terms of pharmacology, toxicity, pharmacokinetics, metabolism, etc. Since racemic drugs have only one bioactive enantiomer while its counterpart enantiomers impart undesirable pharmacological properties, it is necessary to separate these racemic compounds to obtain the desired active enantiomer. Chromatography is one of the approaches for the separation of enantiomers. In this study, we observed the chromatographic profile of racemic mandelic acid compound passed through a chiral HPLC column. The chromatogram profile was then observed computationally to study the separation mechanism. The experimental results are in line with the computational analysis that the S chromatogram eluted first compared to the R-enantiomer. It can be predicted that the binding energy of the R-enantiomer (-108.92 kJ/mol) is stronger than the S-enantiomer (- 67 kJ/mol).</p><p><strong>Methods: </strong>The chromatogram profile of mandelic acid racemate was observed experimentally using a chiral OD column, and the prediction of column-ligand binding energy was based on computational studies using the conformer-rotamer ensemble sampling tool (CREST). The chromatogram profile was identified using a 0.46 cm × 25 cm chiral OD column HPLC instrument (Daicel Chemical). The samples used were racemic compounds of mandelic acid and standard (S)-mandelic acid. Computational calculations of column capacity factors and binding energies of each enantiomer were performed with a Windows 11 Pro 64-bit operating system, × 64-based processor, equipped with the MGL-Tools program consisting of the ADT (Autodock Tools) application, Avogadro, AutoDock 4.2, Discovery Studio 2020 Client®, and CREST installed as a driver program for the XTB semiempirical quantum chemistry package. For geometry optimization and sampling of DMPC-ligand complexes, we used CREST at https://github.com/grimme-lab/crest .</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"206"},"PeriodicalIF":2.1,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615706","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":"Prediction of enzyme inhibition (IC₅₀) using a combination of protein-ligand docking and semiempirical quantum mechanics.","authors":"Robert C Glen, Jason C Cole, James J P Stewart","doi":"10.1007/s00894-025-06423-7","DOIUrl":"10.1007/s00894-025-06423-7","url":null,"abstract":"<p><strong>Context: </strong>The ability to predict the relative binding energies of ligands to a biological receptor would be of great value in drug discovery. However, accurately calculating the predicted binding energies is limited by the high accuracy required, by the presence of multiple minima on the potential energy surface, and by issues specific to the intrinsic properties of the binding site, such as details of the geometry of the ligand-protein complex. To address these issues, a systematic analysis of potential sources of error was carried out which resulted in a few relatively small changes being made to the MOPAC program.</p><p><strong>Methods: </strong>A set of 77 ligands was constructed for which experimentally determined IC₅₀ values were available. For each of the ligands, prediction of the protein-ligand interaction energy was carried out in two distinct stages. In the first stage, the Protein-Ligand docking program GOLD was used to generate several distinct conformations of the ligand bound to a protein. The geometries of these systems were then optimised using the MOPAC program. A comparison of the relative binding energies of the ligands with the reported IC₅₀ values showed a very poor predictive power. By partitioning the ligand set into two subsets, and eliminating six ligands that were inconsistent with the experimental results, a large increase in accuracy was obtained.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"209"},"PeriodicalIF":2.1,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ab initio prediction for product stereo-specificity in the CH₃CHI + O₂ reaction: formation of syn- vs anti-CH₃CHOO.","authors":"Hue-Phuong Trac, Putikam Raghunath, Ming-Chang Lin","doi":"10.1007/s00894-025-06426-4","DOIUrl":"10.1007/s00894-025-06426-4","url":null,"abstract":"<p><strong>Context: </strong>The stereo-specific production of syn- and anti-CH₃CHOO conformers from the CH₃CHI + O₂ reaction has been investigated by ab initio quantum-chemical and statistical theory studies. The results of the studies clearly indicate that the [syn]:[anti] product ratio depends on both temperature and pressure of the reaction system, and is kinetically, rather than thermodynamically, controlled. Most experimental data measured near room temperature at 2-10 Torr He pressure agree with the predicted results in terms of either the absolute rate constants for syn- and anti-CH₃CHOO production and/or the [syn]:[anti] product ratio. If the stereo-specificity of syn- and anti-CH₃CHOO formation were controlled thermodynamically, one would predict [syn]:[anti] = 241:1 independent of pressure at 298 K, instead of (80 ± 10):(20 ± 10) measured experimentally or 86:14 predicted theoretically at 5-Torr He pressure.</p><p><strong>Methods: </strong>All calculations were performed using Gaussian 16 software. Geometry, frequency, and IRC analysis calculations were conducted at the B3LYP/Aug-cc-PVTZ level of theory. The potential energy surface of the system was computed at the CCSD(T)/Aug-cc-PVTZ//B3LYP/Aug-cc-PVTZ level. The rate constants for individual product channels in the reaction, including the direct production of IO + CH₃CHO and the collisional deactivation of the excited CH₃CHIO₂* intermediate formed by the association of CH₃CHI with O₂, were predicted by statistical theory calculations using the Variflex code.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"205"},"PeriodicalIF":2.1,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12254064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regioisomerism effects on the thermal decomposition mechanism of fused triazole-based high-nitrogen compounds: a DFT study.","authors":"Zhihui Gu, Mengjie Bo, Zikai Gao, Congming Ma, Peng Ma","doi":"10.1007/s00894-025-06427-3","DOIUrl":"https://doi.org/10.1007/s00894-025-06427-3","url":null,"abstract":"<p><strong>Context: </strong>High-nitrogen fused-ring compounds are promising candidates for energetic materials due to their high energy density and good thermal stability. As a molecular design strategy, regioisomerism has been widely applied in pharmaceuticals and functional materials. However, its effect on the performance of high-nitrogen fused energetic materials has not yet been systematically investigated. In this study, density functional theory (DFT) was employed to explore the structural and energetic implications of regioisomerism by examining four representative compounds: 3-nitro-1H-[1,2,4]triazolo[4,3-b][1,2,4]triazole (A1), 6-nitro-1H-[1,2,4]triazolo[4,3-b][1,2,4]triazole (A2), [1,2,4]triazolo[4,3-a][1,3,5]triazine-3,5,7-triamine (B1), and [1,2,4]triazolo[1,5-a][1,3,5]triazine-2,5,7-triamine (B2). A comparative analysis was conducted from multiple perspectives, including molecular conformation, bond strength, non-covalent interactions, and surface electrostatic potential distributions. Computational results revealed notable differences among the regioisomers in terms of internal steric repulsion, key bond strength, and charge distribution, which in turn influenced their initial decomposition pathways and corresponding energy barriers. Specifically, A2 and B2 exhibited more compact molecular geometries, reduced intramolecular repulsion, and generally higher activation barriers along key bond cleavage pathways, indicating superior thermal stability compared to their respective isomers. This work highlights the important role of regioisomerism in tuning the thermal stability of high-nitrogen fused-ring energetic compounds and provides theoretical guidance for the rational design of high-performance energetic materials.</p><p><strong>Methods: </strong>All computations in this study were performed using Gaussian 16 at the M06-2X/def2-TZVPP level of theory. The intrinsic reaction coordinate (IRC) calculations were conducted to verify the validity of all transition states. The Shermo program was employed to compute the Gibbs free energy of the molecules, while wavefunction analysis was carried out using Multiwfn and VMD.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":"204"},"PeriodicalIF":2.1,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582780","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}