Journal of Molecular Modeling最新文献

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A comprehensive study of the influence of non-covalent interactions on electron density redistribution during the reaction between acetic acid and methylamine 醋酸与甲胺反应过程中非共价相互作用对电子密度重分布影响的综合研究
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-14 DOI: 10.1007/s00894-024-06249-9
Olivier Aroule, Emilie-Laure Zins
{"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}
引用次数: 0
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) 升温速率对1,3,5-三氨基-2,4,6-三硝基苯(TATB)热分解过程影响的分子动力学模拟研究
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-14 DOI: 10.1007/s00894-024-06270-y
Xianfeng Wei, Shan Sha, Qingying Duan
{"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}
引用次数: 0
Correction to: Constructing, in silico, molecular self‑aggregates and micro‑hydrated complexes of oxirene and thiirene 修正:用硅构建分子自聚集体和环氧乙烷和硫脲的微水合配合物
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-13 DOI: 10.1007/s00894-025-06280-4
Dipali N. Lande, Shridhar P. Gejji, Rajeev K. Pathak
{"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}
引用次数: 0
Study on the modulation mechanism of the optoelectronic properties based on common electrode metal atom adsorption on graphene/MoTe2 基于石墨烯/MoTe2共电极金属原子吸附的光电性能调制机制研究
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-13 DOI: 10.1007/s00894-024-06268-6
Jiabin Li, Nan Yang, Zenghui Fan, Jiang Wang, Yinghang Lei
{"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/MoTe<sub>2</sub> 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/MoTe<sub>2</sub> 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/MoTe<sub>2</sub>. 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/MoTe<sub>2</sub> exhibits significant absorption in the ultraviolet range. Once graphene/MoTe<sub>2</sub> 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/MoTe<sub>2</sub> 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/MoTe<sub>2</sub> consists of 4 × 4 × 1 single-layer, graphene single layer, and 3 × 3 × 1 single-layer MoTe<sub>2</sub>. 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<sup>−5</sup> 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}
引用次数: 0
Towards a unified fold-cusp model for bond polarity scaling: electron rearrangements in the pyrolytic isomerization of cubane to cyclooctatetraene 键极性缩放的统一折尖模型:立方烷裂解异构化成环四烯过程中的电子重排
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-13 DOI: 10.1007/s00894-024-06229-z
Leandro Ayarde-Henríquez, Cristian Guerra, Patricia Pérez, Eduardo Chamorro
{"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<sup>−5</sup>] au interval correlate with cusp unfolding, whereas fold spans over a broader [10<sup>−3</sup>, ∞) 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}
引用次数: 0
Molecular structure characteristic of coals of different rank 不同阶煤的分子结构特征
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-13 DOI: 10.1007/s00894-024-06272-w
Xiulin Shang, Zhongqi Wei, Di Tang, Zhijun Zhang
{"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 <sup>13</sup>C 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 C<sub>193</sub>H<sub>178</sub>N<sub>2</sub>O<sub>47</sub>, that of YQ was C<sub>201</sub>H<sub>179</sub>N<sub>3</sub>O<sub>30</sub>S, and that of TX was C<sub>198</sub>H<sub>118</sub>N<sub>2</sub>O<sub>10</sub>. 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}
引用次数: 0
Comment on: “Energy spectrum of selected diatomic molecules (H(_2), CO, I(_2), NO) by the resolution of Schrödinger equation for combined potentials via NUFA method” 点评:“用NUFA方法解析Schrödinger联合势方程所选双原子分子(H (_2), CO, I (_2), NO)的能谱”
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-10 DOI: 10.1007/s00894-024-06257-9
Francisco M. Fernández
{"title":"Comment on: “Energy spectrum of selected diatomic molecules (H(_2), CO, I(_2), NO) by the resolution of Schrödinger equation for combined potentials via NUFA method”","authors":"Francisco M. Fernández","doi":"10.1007/s00894-024-06257-9","DOIUrl":"10.1007/s00894-024-06257-9","url":null,"abstract":"<div><p>Quantum mechanics has proved to be suitable for the study of molecular systems. In particular, the Born-Oppenheimer approximation enables one to separate the motions of electrons and nuclei. In the case of diatomic molecules, this approximation leads to the so-called potential-energy function that provides the interaction between the two nuclei. There have recently been great misconceptions about the meaning of certain features of the potential-energy function like the equilibrium bond length and dissociation energy. We discuss the meaning of equilibrium bond length and dissociation energy in the case of a potential-energy curve recently proposed for the treatment of diatomic molecules. It consists of the sum of an inverse quadratic Yukawa potential and two screened Coulomb potentials. Our analysis shows that this potential exhibits obvious inconsistencies and that there is a simple way of rewriting it in a correct way. Our procedure is based on the application of well-known definitions of the molecular parameters just mentioned.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938825","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}
引用次数: 0
Theoretical study on highly nitrated sensitive pyrazole isomers in the presence of external electric field 外电场作用下高硝化敏感吡唑异构体的理论研究
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-08 DOI: 10.1007/s00894-024-06271-x
Mengjie Bo, Zikai Gao, Zhihui Gu, Congming Ma, Peng Ma
{"title":"Theoretical study on highly nitrated sensitive pyrazole isomers in the presence of external electric field","authors":"Mengjie Bo,&nbsp;Zikai Gao,&nbsp;Zhihui Gu,&nbsp;Congming Ma,&nbsp;Peng Ma","doi":"10.1007/s00894-024-06271-x","DOIUrl":"10.1007/s00894-024-06271-x","url":null,"abstract":"<div><h3>Context</h3><p>This article mainly studies three isomers of C<sub>5</sub>H<sub>3</sub>N<sub>7</sub>O<sub>10</sub>, namely 5-methyl-3,4-dinitro-1- (trinitromethyl) -1H pyrazole (<b>1</b>), 4-methyl-3,5-dinitro-1- (trinitromethyl) -1H pyrazole (<b>2</b>), and 3,5-bis (dinitromethyl) -4-nitro-1H-pyrazole (<b>3</b>). These three substances are excellent candidates for energetic materials, but their properties under external electric fields (EEF) have not been studied. Therefore, this article studied the properties of three isomers under EEF using density functional theory (DFT), and conducted statistical analysis on the obtained data, including the molecular structure, frontier molecular orbitals, surface electrostatic potential, and nitrate charge of the three isomers. The results showed that applying EEF to the trigger bonds of <b>1</b> and <b>2</b> increased bond length, leading to a decrease in material stability. The change in bond length induced by <b>3</b> was relatively stable, and the results obtained from calculating the nitro charge were consistent with the bond length results. When an EEF is applied to three substances, the polarization degree of the molecules of the three substances increases. It is worth mentioning that the polarization degree of the molecules under the influence of a negative EEF is greater than that of a positive EEF.</p><h3>Methods</h3><p>Using density functional theory, the B3LYP/6–311 + G (d, p) method was employed for structural optimization. After optimizing convergence, ensure that there are no imaginary frequencies to obtain a stable structure. Wave function analysis was performed using Multiwfn 3.8 and VMD 1.9.3. The EEF strength ranged from − 0.02 a.u. to 0.02 a.u., with a growth gradient of 0.005 a.u.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938969","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}
引用次数: 0
π-π stacking interactions in tryptophan-lumiflavin-tyrosine: a structural model for riboflavin insertion into riboflavin-binding protein 色氨酸-荧光黄素-酪氨酸π-π堆叠相互作用:核黄素插入核黄素结合蛋白的结构模型
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-08 DOI: 10.1007/s00894-024-06233-3
Simona Marincean, Moina Al-Modhafir, Daniel B. Lawson
{"title":"π-π stacking interactions in tryptophan-lumiflavin-tyrosine: a structural model for riboflavin insertion into riboflavin-binding protein","authors":"Simona Marincean,&nbsp;Moina Al-Modhafir,&nbsp;Daniel B. Lawson","doi":"10.1007/s00894-024-06233-3","DOIUrl":"10.1007/s00894-024-06233-3","url":null,"abstract":"<div><h3>Context</h3><p>Riboflavin (RF), also known as B2 vitamin, is the precursor to flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), two co-enzymes involved in many electron transport processes. Interactions of the isoalloxazine ring, common to all three compounds, are of great interest due to their biological function in flavoproteins and relevance in the transport by the carrier protein leading to development of drug delivery strategies and non-invasive diagnostics techniques. Based on protein crystallographic data, a computational investigation of the interactions in the complexes between lumiflavin, a model compound, and aromatic amino acids, tyrosine and tryptophan, was pursued with the goal of characterizing noncovalent interactions. Density functional theory (DFT) served as the computation framework for all calculations, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6–311+ +g** basis set. The solvation effects were incorporated through the implementation of the polarizable continuum model (PCM) simulating an aqueous solvent environment. The geometries of the five most stable complexes show exclusively p-p interactions among the aromatic moieties in a displaced parallel plane stacking arrangement with interplanar heights and displacements in the range of 3.22–3.62 Å and 0.50–0.63 Å, respectively, at ωB97XD level. The calculated total energies and binding energies indicate two stabilizing p-p interactions: lumiflavin-tyrosine and lumiflavin-tryptophan, with the later stronger for the more stable complexes by 2 kcal mol<sup>−1</sup>. The complexes are less entropically favored than the independent molecules as verified by the positive association free Gibbs energies with LC-ωPBE and nearly zero with ωB97XD. Orbital analysis indicates a smaller HOMO–LUMO gap for complexes compared to the individual compounds suggesting a charge transfer component to the interaction. Moreover, the HOMO is localized on tryptophan and HOMO-1 on tyrosine, consistent with the strength of the respective interactions with lumiflavin.</p><h3>Methods</h3><p>The initial geometry was based on the atom coordinates of the bonding tryptophan-riboflavin-tyrosine region in the protein crystallographic data with the ribityl tail being discarded, leading to a model complex: tryptophan-lumiflavin-tyrosine. The initial conformational search using the Amber force field within the Gabedit led to 30 unique conformations. The subsequent calculations, energy optimization and orbital analysis, were performed in Guassian16 at density functional theory (DFT) level, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6–311+ +g** basis set. The solvent, water, was accounted for using the polarized continuum model (PCM).</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938971","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}
引用次数: 0
Transition state theoretical modelling of molecular diffusion within the narrow pores of brewsterite zeolite 小沸石窄孔内分子扩散的过渡态理论模拟
IF 2.1 4区 化学
Journal of Molecular Modeling Pub Date : 2025-01-08 DOI: 10.1007/s00894-024-06273-9
Yali Feng, Fang Zhao, Xiaofeng Yang
{"title":"Transition state theoretical modelling of molecular diffusion within the narrow pores of brewsterite zeolite","authors":"Yali Feng,&nbsp;Fang Zhao,&nbsp;Xiaofeng Yang","doi":"10.1007/s00894-024-06273-9","DOIUrl":"10.1007/s00894-024-06273-9","url":null,"abstract":"<div><h3>Context</h3><p>Based on the transition state theory, a molecular diffusion model in the narrow channels of Brewsterite zeolite was established. In this model, the molecular interaction at the potential barrier was simplified to only consider the repulsive potential, so that the analytical relationship between the diffusion coefficient and the temperature and the Lennard–Jones interaction parameter was derived. We used the molecular dynamics method to simulate the diffusion of four molecules, CF<sub>4</sub>, CH<sub>4</sub>, Ar, and Ne, in Brewsterite zeolite and evaluated the rationality of the model. The results show that the three molecules CF<sub>4</sub>, CH<sub>4</sub>, and Ar meet the predictions of the model, while the Ne molecule does not. At the same time, by analyzing the trend of the diffusion coefficient with the load, we further explain the reason for this difference. In short, this study reveals the diffusion mechanism of molecules in the narrow pores of Brewsterite zeolite. This provides new ideas for optimizing the performance of zeolite materials and applying them to catalysis and separation processes.</p><h3>Methods</h3><p>The simulations were carried out with Refson’s MOLDY code in the NVT ensemble. The short-range Lennard–Jones forces were calculated with the link cell method. A Nose–Hoover thermostat was used to realize the thermal equilibrium state of the samples. In the simulation, the time steps were 1 fs and the total simulation time was 51 ns. The initial temperature was set to 300 K.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142938970","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}
引用次数: 0
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