Journal of Molecular Modeling最新文献_第7页

Influence of polypropylene fibers on the tensile mechanical properties of calcium silicate hydrate: molecular simulation 聚丙烯纤维对硅酸钙水合物拉伸机械性能的影响：分子模拟。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-10-02 DOI: 10.1007/s00894-024-06164-z

Yu Chen, Xuyang Yin, Ndukeabasi Peter Udoessiet, Jiale Wang, Jiawen Zhu, Shimei Luo

Context

This research assesses the influence of polypropylene (PP) fibers, both homopolymer and hydroxylated (PPOH), on the tensile properties of calcium silicate hydrate (C-S–H) composites through molecular dynamics (MD) simulations. Our models explore C-S–H matrices integrated with PP and PPOH fibers at varying polymerization degrees. The results demonstrate that both PP and PPOH fibers significantly influence the tensile strength and Young’s modulus of the composites. Notably, PPOH fibers contribute to more substantial mechanical enhancements than PP, attributed to the increased polarity and enhanced intermolecular interactions from the hydroxyl groups. The study reveals a nonlinear relationship between polymer additive content and mechanical performance, with optimal properties at a polymerization degree of 20. Additionally, stress–strain analysis indicates that PPOH composites exhibit superior ductility and fracture energy, particularly at polymerization degrees of 20, showing enhanced ultimate strain and fracture energy by up to 9.6% and 13.9%, respectively, compared to PP counterparts. These results highlight the crucial role of tailored polymer additive composition and chemical modifications in maximizing the mechanical efficacy of C-S–H-based materials, enhancing their durability and structural performance.

Methods

All MD simulations were conducted using LAMMPS. The models employed a combination of Clayff and Cvff force fields. During the entire tensile simulation, the system was configured under the NPT ensemble at 300 K.

背景：本研究通过分子动力学（MD）模拟评估了聚丙烯（PP）纤维（均聚丙烯和羟基化聚丙烯）对水合硅酸钙（C-S-H）复合材料拉伸性能的影响。我们的模型探索了在不同聚合度下与 PP 和 PPOH 纤维集成的 C-S-H 基体。结果表明，PP 和 PPOH 纤维对复合材料的拉伸强度和杨氏模量都有显著影响。值得注意的是，与聚丙烯相比，PPOH 纤维的机械性能增强更为明显，这归因于羟基的极性增强和分子间相互作用的增强。研究表明，聚合物添加剂含量与机械性能之间存在非线性关系，聚合度为 20 时性能最佳。此外，应力应变分析表明，PPOH 复合材料表现出卓越的延展性和断裂能，尤其是在聚合度为 20 时，与 PP 复合材料相比，极限应变和断裂能分别提高了 9.6% 和 13.9%。这些结果凸显了量身定制的聚合物添加剂成分和化学改性在最大限度地提高 C-S-H 基材料的机械功效、增强其耐久性和结构性能方面的关键作用：所有 MD 模拟均使用 LAMMPS 进行。模型采用了 Clayff 和 Cvff 力场组合。在整个拉伸模拟过程中，系统均配置在 300 K 的 NPT 组合下。

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引用次数: 0

Development of new sustainable pyridinium ionic liquids: From reactivity studies to mechanism-based activity predictions 新型可持续吡啶离子液体的开发：从反应性研究到基于机理的活性预测。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-10-02 DOI: 10.1007/s00894-024-06157-y

Bakhtiyor Borikhonov, Elyor Berdimurodov, Tursunali Kholikov, W. B. Wan Nik, Konstantin P. Katin, Muslum DEMİR, Frunza Sapaev, Sherzod Turaev, Nigora Jurakulova, Ilyos Eliboev

Context

This study addresses the development of sustainable pyridinium ionic liquids (ILs) because of their potential applications in agriculture and pharmaceuticals. Pyridinium-based ILs are known for their low melting points, high thermal stability, and moderate solvation properties. We synthesized three novel pyridinium-based ILs: 1-(2-(isopentyloxy)-2-oxoethyl)pyridin-1-ium chloride, 1-(2-(hexyloxy)-2-oxoethyl)pyridin-1-ium chloride, and 1-(2-(benzyloxy)-2-oxoethyl)pyridin-1-ium chloride. The biological activities of these compounds were evaluated through plant growth promotion, herbicidal, and insecticidal assays. Our results show that the benzyloxy derivative significantly enhances wheat and cucumber growth, whereas the isopentyloxy compound has potent herbicidal effects. Computational methods, including DFT calculations and molecular docking, were applied to understand the structure‒activity relationships (SARs) and mechanisms of action.

Methods

The computational techniques involved dispersion-corrected density functional theory (DFT) with the B3LYP functional and the 6-311G** basis set. Grimme’s D3 corrections were included to account for dispersion interactions. The calculations were performed via GAMESS-US software. Quantum descriptors of reactivity, such as ionization potential, electron affinity, chemical potential, and electrophilicity index, were derived from the HOMO and LUMO energies. Molecular docking studies were conducted via the CB-Dock server via AutoDock Vina software to predict binding affinities to cancer-related proteins. Petra/Osiris/Molinspiration (POM) analysis was used to predict the drug likeness and other pharmaceutical properties of the synthesized ILs.

背景：由于吡啶鎓离子液体（ILs）在农业和制药领域具有潜在的应用前景，本研究旨在开发可持续的吡啶鎓离子液体（ILs）。吡啶鎓离子液体以其低熔点、高热稳定性和适中的溶解特性而著称。我们合成了三种新型吡啶基 IL：1-(2-(异戊氧基)-2-氧代乙基)吡啶-1-鎓氯化物、1-(2-(己氧基)-2-氧代乙基)吡啶-1-鎓氯化物和 1-(2-(苄氧基)-2-氧代乙基)吡啶-1-鎓氯化物。这些化合物的生物活性通过植物生长促进、除草和杀虫实验进行了评估。结果表明，苄氧基衍生物能显著促进小麦和黄瓜的生长，而异戊氧基化合物则具有很强的除草作用。我们采用了包括 DFT 计算和分子对接在内的计算方法来了解其结构-活性关系（SARs）和作用机制：计算技术包括采用 B3LYP 函数和 6-311G** 基集的色散校正密度泛函理论（DFT）。为了考虑弥散相互作用，还加入了 Grimme 的 D3 修正。计算通过 GAMESS-US 软件进行。反应性的量子描述符，如电离势、电子亲和力、化学势和亲电指数，都是从 HOMO 和 LUMO 能量中推导出来的。通过 CB-Dock 服务器和 AutoDock Vina 软件进行了分子对接研究，以预测与癌症相关蛋白的结合亲和力。Petra/Osiris/Molinspiration (POM) 分析用于预测合成的 ILs 的药物相似性和其他药物特性。

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引用次数: 0

Approximate resolutions of the Schrodinger theory applying the WKB approximation for certain diatomic molecular interactions 应用 WKB 近似值对某些二原子分子相互作用的薛定谔理论进行近似解析。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-30 DOI: 10.1007/s00894-024-06143-4

Khalid Reggab

Context

The Analyzing of energetic bond spectra of diatomic compounds is crucial to understanding their qualities because it allows one to evaluate their attributes. Diatoms compounds' spectral properties and bound energies are presented in this study. These energies are found by solving the Schrodinger equation while making consideration of the employing of the Kratzer Feus potential.

Method

This study focuses on the calculation of bound states for diatomic molecules using the WKB approximation. The final energy spectrum equation is utilized to compute the bound states of specific diatomic molecules for varying quantum numbers n and l through the utilization of the Mathematica software. The method produced the desired and anticipated results, as shown by a comparison of the eigenvalue results with earlier studies.

背景：分析二原子化合物的能键光谱对了解其质量至关重要，因为这可以评估其属性。本研究介绍了硅藻化合物的光谱特性和结合能。这些能量是在考虑使用 Kratzer Feus 势的情况下，通过求解薛定谔方程得到的：方法：本研究侧重于使用 WKB 近似法计算二原子分子的束缚态。通过使用 Mathematica 软件，利用最终能谱方程计算特定二原子分子在不同量子数 n 和 l 条件下的束缚态。通过将特征值结果与先前的研究结果进行比较，可以看出该方法产生了预期的结果。

引用次数: 0

Tuning optoelectronic properties of indandione-based D-A materials by malononitrile group acceptors: A DFT and TD-DFT approach 通过丙二腈基团受体调谐茚二酮基 D-A 材料的光电特性：DFT 和 TD-DFT 方法。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-30 DOI: 10.1007/s00894-024-06159-w

Pankaj Kumar Kushwaha, Sunil Kumar Srivastava

Context

Indandione-based materials are promising candidates for organic electronics, offering high electron mobility and tunable optoelectronic properties. In this study, we explore the optoelectronic and photovoltaic properties of indandione-based donor–acceptor (D-A) materials, specifically (R1) and (R2), by introducing malononitrile group acceptors into their molecular structure. These strong electron-withdrawing acceptors are designed to enhance charge transfer and overall material performance. The designed molecules (DM1–DM4) exhibit a low optical band gap of approximately 1.77 eV, significantly lower than the reference materials (R1 and R2) at around 2.24 eV in a solvent environment. Among the designed molecules, DM4 stands out with superior photovoltaic parameters, including a narrow optical band gap (1.77 eV), higher electron affinity (3.49 eV), an extended excited state lifetime (10.0 ns) owing to its low electron and hole reorganization energies (λ_e ~ 0.13 eV and λ_h ~ 0.24 eV), and improved short-circuit current density (J_sc) of ~ 15.73 mA/cm². Notably, DM4 achieves a power conversion efficiency (PCE) of ~ 18.5%, making it an excellent candidate for device applications.

Method

A comprehensive computational investigation was carried out on indandione-based D-A materials with malononitrile group acceptors (DM1–DM4) using density functional theory (DFT) and time-dependent DFT (TD-DFT) methods, as implemented in Gaussian 16 software. We examined the electronic and optical properties of the proposed molecules through frontier molecular orbital (FMO) analysis, UV–Vis absorption spectra, density of states (DOS), exciton binding energy (E_b), and transition density matrix (TDM) analysis, utilizing GaussView 6.0 and Multiwfn 3.8 software. The photovoltaic parameters and power conversion efficiency (PCE) were evaluated using the Scharber and Alharbi models.

背景：茚二酮基材料具有高电子迁移率和可调光电特性，是有机电子学的理想候选材料。在本研究中，我们通过在分子结构中引入丙二腈基团受体，探索了基于茚二酮的供体-受体（D-A）材料，特别是（R1）和（R2）的光电和光伏特性。这些强电子吸收受体旨在增强电荷转移和材料的整体性能。设计的分子（DM1-DM4）显示出约 1.77 eV 的低光带隙，明显低于溶剂环境中约 2.24 eV 的参考材料（R1 和 R2）。在所设计的分子中，DM4 的光电参数尤为突出，包括较窄的光带隙（1.77 eV）、较高的电子亲和力（3.49 eV）、因其较低的电子和空穴重组能（λe ~ 0.13 eV 和 λh ~ 0.24 eV）而延长的激发态寿命（10.0 ns），以及较高的短路电流密度（Jsc）（约 15.73 mA/cm2）。值得注意的是，DM4 的功率转换效率（PCE）达到了约 18.5%，是器件应用的绝佳候选材料：采用密度泛函理论（DFT）和时间相关 DFT（TD-DFT）方法，对带有丙二腈基团受体的茚二酮基 D-A 材料（DM1-DM4）进行了全面的计算研究。我们利用 GaussView 6.0 和 Multiwfn 3.8 软件，通过前沿分子轨道 (FMO) 分析、紫外-可见吸收光谱、状态密度 (DOS)、激子结合能 (Eb) 和跃迁密度矩阵 (TDM) 分析，研究了拟议分子的电子和光学特性。利用 Scharber 和 Alharbi 模型对光伏参数和功率转换效率（PCE）进行了评估。

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引用次数: 0

Transition from synchronous to asynchronous mechanisms in 1,3-dipolar cycloadditions: a polarizability perspective 1,3-二极环加成反应中从同步到异步机制的转变：极化性视角。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-30 DOI: 10.1007/s00894-024-06161-2

César Barrales-Martínez, Rocío Durán, Pablo Jaque

Context

This study investigates the energetic and polarizability characteristics of three 1,3-dipolar cycloaddition reactions between diazene oxide and substituted ethylenes, focusing on the transition from synchronous to asynchronous mechanisms. Synchronicity analysis, using the reaction force constant, indicates that the bond evolution process becomes increasingly decoupled as the number of cyano groups increases. Polarizability analysis reveals that isotropic polarizability reaches its maximum near the transition state in all cases, while anisotropy of polarizability shifts from the transition state toward the product direction as asynchronicity increases. The larger the shift, the more asynchronous the mechanism, as reflected by the weight of the transition region. A detailed examination of the parallel and perpendicular polarizability components to the newly formed sigma bonds shows that the evolution of the parallel component is closely aligned with the energetic changes along the reaction coordinate, particularly in the synchronous reaction. We have also identified a relationship between the displacement in the maximum state of the parallel component from the transition state and the synchronicity of the mechanism. The larger the displacement, the more asynchronous the mechanism. These findings suggest that asynchronous 1,3-dipolar cycloaddition mechanisms are characterized by a decoupling of isotropic and anisotropic polarizabilities and a shift in the maximum polarizability state of the parallel component toward the product direction.

Methods

Density functional theory calculations were performed at the B3LYP/6–311 + + G(d,p)//B3LYP/6-31G(d,p) level of theory. The polarizability was calculated at each point of the reaction path, obtained using the intrinsic reaction coordinate method, as implemented in Gaussian 16.

背景：本研究探讨了氧化二氮烯和取代乙烯之间的三个 1,3-二极环加成反应的能量和极化特性，重点是同步机制向异步机制的过渡。利用反应力常数进行的同步性分析表明，随着氰基数量的增加，键的演化过程变得越来越非耦合。极化性分析表明，在所有情况下，各向同性的极化性都在过渡态附近达到最大值，而随着异步性的增加，极化性的各向异性从过渡态向产物方向移动。转变越大，机制越不同步，这一点可以从过渡区域的权重反映出来。对新形成的西格玛键的平行和垂直极化率分量的详细研究表明，平行分量的演变与沿反应坐标的能量变化密切相关，尤其是在同步反应中。我们还发现了平行分量从过渡态到最大态的位移与机理同步性之间的关系。位移越大，机制越不同步。这些发现表明，异步 1,3-二极环加成机制的特点是各向同性和各向异性极化率的解耦，以及平行组分的最大极化率状态向产物方向的移动：密度泛函理论计算是在 B3LYP/6-311 + + G（d，p）//B3LYP/6-31G（d，p）理论水平上进行的。使用高斯 16 中的固有反应坐标法计算了反应路径上每一点的极化率。

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引用次数: 0

Hydrophenoxylation of alkynes by gold catalysts: a mini review 金催化剂对炔烃的氢化苯氧基化：小型综述。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-30 DOI: 10.1007/s00894-024-06152-3

Miguel Ramos, Miquel Solà, Albert Poater

Context

The field of chemistry has significantly evolved, with catalysis playing a crucial role in transforming chemical processes. From Valerius’ use of sulfuric acid in the sixteenth century to modern advancements, catalysis has driven innovations across various industries. The introduction of gold as a catalyst marked a pivotal shift, expanding its applications beyond ornamentation to homogeneous catalysis. Gold’s unique properties, such as its electrophilic nature and flexibility, have enabled its use in synthesizing complex molecules, including those in nanomedicine and sustainable chemical processes. The development of gold-based complexes, particularly in hydroalkoxylation and hydroamination reactions, showcases their efficiency in forming carbon–oxygen bonds under mild conditions. Recent studies on dual gold catalysis and heterobimetallic complexes further highlight gold’s versatility in achieving high turnover rates and selectivity. This evolution underscores the potential of gold catalysis in advancing environmentally sustainable methodologies and enhancing the scope of modern synthetic chemistry. The debate about the nature of monogold and dual-gold catalysis is open.

Methods

DFT calculations have played a key role in promoting the activation of alkynes, in particular the hydrophenoxylation of alkynes by metal-based catalysts. They not only help identify the most efficient and selective catalysts but also aid in screening for those capable of performing a dual metal catalytic mechanism. The most commonly used functionals are BP86 and B3LYP, with the SVP and 6-31G(d) basis sets employed for geometry optimizations, and M06 with TZVP or 6-311G(d,p) basis sets used for single-point energy calculations in a solvent. Grimme dispersion correction has been explicitly added either in the solvent single point energy calculations or in the gas phase geometry optimizations or in both. To point out that M06 implicitly includes part of this dispersion scheme.

背景：催化在化学过程的变革中发挥着至关重要的作用。从十六世纪 Valerius 使用硫酸到现代催化技术的进步，催化技术推动了各行各业的创新。金作为催化剂的问世标志着一个关键性的转变，将其应用范围从装饰品扩展到均相催化。金的独特性质，如亲电性和灵活性，使其能够用于合成复杂的分子，包括纳米医学和可持续化学工艺中的分子。金基配合物的开发，特别是在氢烷氧基化和氢化反应中的应用，展示了其在温和条件下形成碳氧键的效率。最近对双重金催化和杂多金属复合物的研究进一步突出了金在实现高转化率和高选择性方面的多功能性。这一演变凸显了金催化在推进环境可持续方法和扩大现代合成化学范围方面的潜力。有关单金催化和双金催化性质的争论尚未结束：DFT 计算在促进炔烃活化，特别是金属催化剂对炔烃的氢化苯氧基化方面发挥了关键作用。它们不仅有助于确定最高效、最具选择性的催化剂，还有助于筛选出能够实现双金属催化机理的催化剂。最常用的函数是 BP86 和 B3LYP，其中 SVP 和 6-31G(d) 基集用于几何优化，M06 和 TZVP 或 6-311G(d,p) 基集用于溶剂中的单点能计算。在溶剂单点能计算或气相几何优化中，或在两者中都明确添加了格里姆弥散校正。需要指出的是，M06 中隐含了该色散方案的一部分。

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引用次数: 0

Investigation of structural, elastic, electronic, and optical properties of lead-free double perovskites Cs2XBeBr6 (X = Ge, Sn): a first-principles DFT study 无铅双包晶石 Cs2XBeBr6 (X = Ge, Sn) 的结构、弹性、电子和光学特性研究：第一原理 DFT 研究。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-29 DOI: 10.1007/s00894-024-06158-x

Messaoud Caid, Habib Rached, Djamel Rached, Youcef Rached

Context

In this study, the structural, elastic, electronic, and optical properties of Cs₂GeBeBr₆ and Cs₂SnBeBr₆ halide double perovskites (HDPs) were investigated using density functional theory (DFT) calculations. Notably, the Tran-Blaha modified Becke-Johnson (TB-mBJ) method was employed to predict indirect band gaps of 2.434 eV for Cs₂GeBeBr₆ and 2.855 eV for Cs₂SnBeBr₆. The stability of these compounds in a cubic (Fm-3m) structure was confirmed through formation energy, cohesive energy, tolerance factor, and elastic constants. Furthermore, the ductile nature of the materials was demonstrated through Poisson's and Pugh's ratios. Our optical property analysis, spanning the 0–13 eV energy range, revealed key insights into the dielectric functions, extinction coefficient, electron energy loss, refractive index, optical conductivity, reflectivity, and absorption coefficient. These results highlight the potential of Cs₂GeBeBr₆ and Cs₂SnBeBr₆ for future optoelectronic and photovoltaic applications.

Methods

In this investigation, we employed density functional theory (DFT), implemented using the Wien2k package. The exchange and correlation potentials were treated using the generalized gradient approximation (GGA) and the Tran-Blaha modified Becke-Johnson (TB-mBJ) method. To evaluate dynamic stability, we analyzed the phonon band structures using the CASTEP code.

背景：本研究采用密度泛函理论（DFT）计算方法研究了 Cs2GeBeBr6 和 Cs2SnBeBr6 卤化物双包晶（HDPs）的结构、弹性、电子和光学性质。值得注意的是，采用 Tran-Blaha 修正贝克-约翰逊（TB-mBJ）方法预测出 Cs2GeBeBr6 和 Cs2SnBeBr6 的间接带隙分别为 2.434 eV 和 2.855 eV。通过形成能、内聚能、容忍因子和弹性常数，证实了这些化合物在立方（Fm-3m）结构中的稳定性。此外，泊松比和普氏比也证明了这些材料的延展性。我们的光学特性分析跨越了 0-13 eV 的能量范围，揭示了介电函数、消光系数、电子能量损失、折射率、光导率、反射率和吸收系数的关键信息。这些结果凸显了 Cs2GeBeBr6 和 Cs2SnBeBr6 在未来光电应用领域的潜力：在这项研究中，我们采用了密度泛函理论（DFT），并通过 Wien2k 软件包实现。采用广义梯度近似（GGA）和 Tran-Blaha 修正贝克-约翰逊（TB-mBJ）方法处理了交换势和相关势。为了评估动态稳定性，我们使用 CASTEP 代码分析了声子带结构。

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引用次数: 0

Temperature and pressure effects on the decomposition mechanisms of 2,6-diamino-3,5-dinitropyrazine-1-oxide crystal: ab initio molecular dynamics study 温度和压力对 2,6-二氨基-3,5-二硝基吡嗪-1-氧化物晶体分解机制的影响：ab initio 分子动力学研究。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-28 DOI: 10.1007/s00894-024-06156-z

Jincheng Ji, Hui Li, Weihua Zhu

Context

The decomposition process of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) crystal at high temperatures (2500 and 3390 K) and detonation pressure of 33.4 GPa coupled with temperatures were studied by ab initio molecular dynamics simulations. The results show that the initial decomposition mechanism of LLM-105 is the same under different conditions. The product analysis indicates that high temperature is conducive to the formation of N₂ and CO₂, but inhibited the formation of H₂O. It is found that the formation mechanism of H₂O is the same under different conditions, which involves the reaction between OH radical and H radical. Although the detailed processes of the formation of N₂ are different, they all involve the reaction between nitrogen-containing fragments, and its core is the formation of intermediates with R₁-NN-R₂ structure. The core of the formation of CO₂ under different conditions is to form the intermediate R₁-CO-R₂ with carbonyl structure, and then generate the fragment with -OCO- structure, and finally generate CO₂. This research may provide new insights into the initiation and subsequent decomposition mechanisms of energetic materials under extreme conditions.

Methods

The LLM-105 supercell was constructed using the Materials Studio 7.0 package. AIMD simulations were performed in the CASTEP package. AIMD simulations adopted NVT and NPT ensemble, and the temperature was controlled by Nosé thermostat, while the pressure was controlled by Andersen barostat. Besides, DFT calculations were carried out at the B3LYP/6–311 + G(d,p) level using the Gaussian 09 package.

背景：通过ab initio分子动力学模拟研究了2,6-二氨基-3,5-二硝基吡嗪-1-氧化物（LLM-105）晶体在高温（2500 K和3390 K）和33.4 GPa爆轰压力与温度耦合条件下的分解过程。结果表明，在不同条件下，LLM-105 的初始分解机理是相同的。产物分析表明，高温有利于 N2 和 CO2 的形成，但抑制了 H2O 的形成。研究发现，H2O 的形成机理在不同条件下是相同的，都涉及 OH 自由基和 H 自由基之间的反应。虽然 N2 形成的具体过程不同，但都涉及含氮片段之间的反应，其核心是形成具有 R1-NN-R2 结构的中间产物。在不同条件下形成 CO2 的核心是形成具有羰基结构的中间体 R1-CO-R2，然后生成具有 -OCO- 结构的片段，最后生成 CO2。这项研究可能会对极端条件下高能材料的起始和后续分解机制提供新的见解：方法：使用 Materials Studio 7.0 软件包构建了 LLM-105 超级椭球体。AIMD模拟在CASTEP软件包中进行。AIMD模拟采用了NVT和NPT集合，温度由诺塞恒温器控制，压力由安德森恒压器控制。此外，还使用高斯 09 软件包在 B3LYP/6-311 + G(d,p) 水平上进行了 DFT 计算。

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引用次数: 0

Rational analysis of hydrogen bonding interaction in phenazine, 2-hydroxynaphthalene (1:1) cocrystal: from molecular modeling to photophysical properties 酚嗪、2-羟基萘（1:1）共晶体中氢键相互作用的理性分析：从分子建模到光物理特性。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-27 DOI: 10.1007/s00894-024-06128-3

T. Sundareswaran, R. Jagan, N. Karthikeyan, B. Milton Boaz

Context

Organic cocrystals have a wide range of applications in the field of optics due to their photo responsive property. We present here a newly synthesized phenazine 2-hydroxynaphthalene (1:1) cocrystal, its structural and theoretical calculations which tend to the nonlinear optical property. In the crystal structure of the title cocrystal, the phenazine and 2-hydroxynaphthalene molecules from one- and two-dimensional supramolecular frameworks via O‒H…N hydrogen bonds and C‒H…N, C‒H…π interaction, respectively. The phenazine molecules from an infinite off-set stacking through π…π interaction in the three-dimensional molecular packing of the title cocrystal. The contribution of intermolecular interaction in the three-dimensional molecular packing and the interaction energy calculation is studied by the Hirshfeld surface analysis. The molecular geometry retrieved from the experimental X-ray diffraction analysis is in good agreement with the theoretically calculated parameters. Further, the molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analysis have been carried out to study the charge distribution and molecular reactive mechanism. Third-order nonlinear optical property of the cocrystals has been analyzed by Z-scan measurements. The determined nonlinear optical absorption coefficient value 6.442 × 10⁻⁰⁵ (m/W) and the nonlinear refractive index value − 5.535 × 10⁻² (m/W) suggest that the crystalline solid can be a good choice of potential nonlinear optical material.

Method

The crystal structures of phenazine 2-hydroxynaphthalene cocrystal was solved by direct methods procedure using SHELXS program and refined by full-matrix least square procedure on F² using SHELXL-2018 program on Olex2 software. The computational calculation has been carried out using DFT/B3LYP quantum chemical function with triple zeta 6–311 + + basis set in the ground state molecular stability using Gaussian 09W program suite. The Hirshfeld surface analysis mapping, associated 2D fingerprint plot, and intermolecular molecular interaction energy calculations were carried out using CrystalExplorer (version 21.5) software.

背景：有机共晶体具有光响应特性，因此在光学领域有着广泛的应用。我们在此介绍一种新合成的酚嗪-2-羟基萘（1:1）共晶体，其结构和理论计算都倾向于非线性光学特性。在该共晶体的晶体结构中，来自一维和二维超分子框架的酚嗪分子和 2-羟基萘分子分别通过 O-H...N 氢键和 C-H...N、C-H...π 相互作用。吩嗪分子通过π...π相互作用在标题共晶体的三维分子堆积中形成无限偏移堆积。通过 Hirshfeld 表面分析，研究了分子间相互作用在三维分子堆积中的贡献以及相互作用能的计算。通过 X 射线衍射实验分析得出的分子几何形状与理论计算参数非常吻合。此外，还进行了分子静电位（MEP）和前沿分子轨道（FMO）分析，以研究电荷分布和分子反应机制。通过 Z 扫描测量分析了共晶体的三阶非线性光学特性。测定的非线性光学吸收系数值为 6.442 × 10-05 (m/W)，非线性折射率值为 - 5.535 × 10-2 (m/W)，这表明该结晶固体是潜在非线性光学材料的良好选择：利用 SHELXS 程序通过直接法程序求解了酚嗪-2-羟基萘共晶的晶体结构，并利用 Olex2 软件上的 SHELXL-2018 程序在 F2 上通过全矩阵最小二乘法程序对晶体结构进行了细化。计算时使用了 DFT/B3LYP 量子化学函数，并在基态分子稳定性方面使用了高斯 09W 程序套件的三重泽塔 6-311 + + 基集。使用 CrystalExplorer（21.5 版）软件进行了 Hirshfeld 表面分析绘图、相关的二维指纹图谱和分子间相互作用能计算。

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引用次数: 0

Analytical potential energy functions for CO(^+) in its ground and excited electronic states CO + 在基态和激发电子态的分析势能函数。

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2024-09-27 DOI: 10.1007/s00894-024-06131-8

Judith P. Araújo, Maikel Y. Ballester, Isadora G. Lugão, Rafael P. Silva, Mariana P. Martins

Context

Accurate functions to analytically represent the potential energy interactions of CO(^+) diatomic system in (mathrm {X^2Sigma ^+}), (mathrm {A^2Pi }), and (mathrm {B^2Sigma ^+}) electronic states are proposed. The new functions depend upon only four parameters directly obtained from experimental data, without any fitting procedure. These functions have been developed from the modified generalized potential proposed by Araújo and Ballester. The function for the (mathrm {X^2Sigma ^+}) electronic state represents a significant improvement to the previously proposed model. To quantify the accuracy of the potential energy functions, the Lippincont test is used. The novel potential was also compared with the classical Morse potential and with the recently proposed Improved Generalized Pöschl-Teller potential. Furthermore, the main spectroscopic constants and vibrational energy levels are calculated and compared for all potentials. The present results agree excellently with the experiment Rydberg-Klein-Rees (RKR) potentials.

Methods

The rovibrational energy levels of the proposed diatomic potentials were asserted by solving radial the Schrödinger equation of the nuclear motion with the aid of the LEVEL program.

背景：提出了精确的函数来分析表示 CO + 双原子系统在 X 2 Σ +、A 2 Π 和 B 2 Σ + 电子状态下的势能相互作用。新函数只依赖于直接从实验数据中获得的四个参数，不需要任何拟合过程。这些函数是由 Araújo 和 Ballester 提出的修正广义电势发展而来的。X 2 Σ + 电子态函数是对之前提出的模型的重大改进。为了量化势能函数的准确性，使用了 Lippincont 检验。新的势能函数还与经典莫尔斯势能函数和最近提出的改进广义波氏-泰勒势能函数进行了比较。此外，还计算并比较了所有势的主要光谱常数和振动能级。目前的结果与实验中的 Rydberg-Klein-Rees (RKR) 电位非常吻合：方法：借助 LEVEL 程序，通过径向求解核运动的薛定谔方程，确定了所提出的二原子势的振动能级。

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