Journal of Molecular Modeling最新文献_第10页

Molecular dynamics simulation of FOX-7 decomposition reaction under high temperature and pressure 高温高压下FOX-7分解反应的分子动力学模拟

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-04 DOI: 10.1007/s00894-025-06497-3

Dandan Li, Wenpeng Wang, Jingzhao Cao, Qijun Liu

Context

The decompositions of FOX-7 under high temperatures (2750–3750 K) and high pressures (0–50 GPa) were investigated using the ReaxFF-lg reactive force field molecular dynamics method, revealing its thermodynamic evolution and product formation mechanisms. The decomposition products are all NO₂, NO, N₂, H₂O, CO₂, HNCO, H₂, CO and NH₃, under high-temperatures and high-pressures conditions. Among these products, the intermediate products are NO₂ and NO, and the stabilization products are N₂, H₂O, CO₂, HNCO, H₂, CO and NH₃. And N₂ is consistently the most abundant product, while HNCO is the least abundant substance. In general, the yield of these products shows a positive correlation with temperature and a negative correlation with pressure. However, NH₃ content increases as pressure rises under high pressures. Additionally, FOX-7’s initial decomposition pathways are: C–NO₂ cleavage (yielding NO₂), N–O rupture (releasing O) and N–H dissociation (releasing H). This paper investigates the thermal decomposition behavior of FOX-7 under extreme conditions of high temperature and high pressure, revealing its decomposition pathway and providing support for the study of the decomposition behavior of other similar substances.

Methods

Molecular dynamics simulations of FOX-7 were performed using Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) with the ReaxFF-lg force field. A 2 × 4 × 2 supercell was constructed based on X-ray diffraction data, optimized geometrically (0.1 fs time step), equilibrated via NVE ensemble (10 ps, heated from 0 to 300 K) and NPT ensemble (15 ps, 300 K), verifying the applicability of ReaxFF-lg. To study high-temperature and high-pressure effects on FOX-7 thermal decomposition, two approaches were used. First, under NVE ensemble, the system was heated to target temperatures (2750—3750 K.) over 150 ps, then maintained for 150 ps (0.1 fs step, periodic boundaries). Second, initial pressures (0–50 GPa) were applied at 300 K via NPT ensemble for 20 ps, followed by heating to 3500 K over 50 ps under NVE. Atomic trajectories, species, and thermodynamic data were recorded every 10 fs.

采用ReaxFF-lg反应力场分子动力学方法研究了FOX-7在高温（2750 ~ 3750 K）和高压（0 ~ 50 GPa）下的分解过程，揭示了其热力学演化和产物形成机理。高温高压条件下的分解产物均为NO2、NO、N2、H2O、CO2、HNCO、H2、CO和NH3。其中，中间产物为NO2和NO，稳定产物为N2、H2O、CO2、HNCO、H2、CO和NH3。N2始终是最丰富的产物，而HNCO是最不丰富的物质。一般来说，这些产物的产率与温度呈正相关，与压力负相关。然而，在高压下，NH3含量随着压力的增加而增加。FOX-7的初始分解途径为：C-NO2裂解（生成NO2）、N-O断裂（释放O）和N-H解离（释放H）。本文研究了FOX-7在高温高压极端条件下的热分解行为，揭示了FOX-7的分解途径，为研究其他类似物质的分解行为提供了支持。方法采用ReaxFF-lg力场的大规模原子/分子大规模并行模拟器（LAMMPS）对FOX-7进行分子动力学模拟。基于x射线衍射数据构建了一个2 × 4 × 2的超级单体，进行了几何优化（0.1 fs时间步长），通过NVE系综（10 ps，从0到300 K加热）和NPT系综（15 ps, 300 K）进行了平衡，验证了ReaxFF-lg的适用性。为了研究高温高压对FOX-7热分解的影响，采用了两种方法。首先，在NVE集成下，将系统加热到目标温度（2750-3750 k）超过150 ps，然后保持150 ps （0.1 fs步长，周期边界）。其次，通过NPT系综在300 K下施加初始压力（0-50 GPa） 20 ps，然后在NVE下加热到3500 K，超过50 ps。每隔10秒记录一次原子轨迹、物质和热力学数据。

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引用次数: 0

In silico identification of anticancer flavonoids as dengue virus replication inhibitors: a molecular docking and simulation approach 抗癌类黄酮作为登革热病毒复制抑制剂的硅鉴定：分子对接和模拟方法

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-04 DOI: 10.1007/s00894-025-06516-3

Soumendu Patra, Arindam Paul, Harshita Shand, Sayan Ghosal, Suvankar Ghorai

<div><h3>Context</h3><p>Dengue, a mosquito-borne viral disease endemic to over 100 countries, poses a serious health risk to people living in tropical regions. The viral non-structural proteins NS3 (helicase) and NS5 (RNA-dependent RNA polymerase) are critical targets for antiviral drug development. Several natural and synthetic compounds have been tried against this for the screening of antiviral inhibitor(s) but so far limited success has been achieved. In this study, we have investigated how natural products interact with and destabilize NS3 and NS5. We used in silico methods to screen new potential NS3 and NS5 inhibitors from various anti-cancer flavonoid compounds that previously showed anti-cancer properties in vitro. A virtual screening was conducted on 329 anti-cancer flavonoid compounds, selecting 190 compounds based on Lipinski’s rule of five, the Muegge filter, the Ghose filter, and the Veber filter. Molecular docking techniques allowed us to identify Artobiloxanthone (PubChem CID: 46887866) as the most effective binder for NS3, while Glabridin (PubChem CID: 124052) emerged as the most effective binder for NS5. These leading candidates demonstrated favorable ADMET profiles. Additionally, molecular dynamics (MD) simulations of up to 1000-ns showcased stable protein–ligand interactions, with convergence achieved at 200 ns for NS3 and 470 ns for NS5. The structural stability of the complexes was validated by analyzing root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bonding (H-bonding). Binding affinity between the ligand and target proteins was further validated by binding free energy calculations using the Molecular Mechanics Poisson–Boltzmann Surface Area (MM-PBSA) approach, providing a robust estimation of interaction stability. These findings highlight the potential of Artobiloxanthone and Glabridin as promising inhibitors of dengue virus replication.</p><h3>Methods</h3><p>The Chimera v1.11.2 program was employed for protein optimization, while PyRx 0.8 served for molecular docking. Protein structures were converted into.pdbqt format, and ligands were energy-minimized using the MMFF94 force field and conjugate gradient optimization. Visualization was conducted using BIOVIA Discovery Studio Visualizer and PyMOL. The ADMET properties of the top hits were predicted using the pkCSM and ProTox-II platforms. To address missing residues in the crystal structures, AlphaFold2 was used to predict full-length protein models. MD simulations were performed with the GROMACS 2024.5 package, utilizing the AMBER-f99SB-ILDN force field, the TIP3P water model, and a 120 mM NaCl concentration. Equilibration was achieved through V-rescale and C-rescale thermostats, followed by Parrinello–Rahman barostat production runs. Analysis of the MD trajectories included RMSD, RMSF, Rg, SASA, H-bonding, and MM-PBSA utilizing GROMACS tools, gmx_MMPBSA, VMD, and MDAna

登革热是一种蚊子传播的病毒性疾病，在100多个国家流行，对生活在热带地区的人们构成严重的健康风险。病毒非结构蛋白NS3（解旋酶）和NS5 （RNA依赖性RNA聚合酶）是抗病毒药物开发的重要靶点。已经尝试了几种天然和合成化合物来筛选抗病毒抑制剂，但迄今为止取得的成功有限。在本研究中，我们研究了天然产物如何与NS3和NS5相互作用并使其失稳。我们利用计算机方法从各种抗癌类黄酮化合物中筛选新的潜在的NS3和NS5抑制剂，这些化合物先前在体外显示出抗癌特性。对329种抗癌类黄酮化合物进行虚拟筛选，根据Lipinski的五法则、Muegge过滤器、Ghose过滤器和Veber过滤器筛选出190种化合物。分子对接技术使我们确定Artobiloxanthone （PubChem CID: 46887866）是NS3最有效的结合剂，而光定（PubChem CID: 124052）是NS5最有效的结合剂。这些领先的候选人表现出良好的ADMET概况。此外，分子动力学（MD）模拟显示，高达1000-ns的蛋白质-配体相互作用稳定，NS3和NS5分别在200 ns和470 ns下实现收敛。通过分析配合物的均方根偏差（RMSD）、均方根波动（RMSF）、旋转半径（Rg）、溶剂可及表面积（SASA）和氢键（h -键）来验证配合物的结构稳定性。利用分子力学泊松-玻尔兹曼表面积（MM-PBSA）方法计算结合自由能，进一步验证了配体与靶蛋白之间的结合亲和力，提供了对相互作用稳定性的可靠估计。这些发现突出了Artobiloxanthone和光定作为登革热病毒复制抑制剂的潜力。方法采用Chimera v1.11.2程序进行蛋白优化，PyRx 0.8程序进行分子对接。蛋白质结构被转化为。采用MMFF94力场和共轭梯度优化对配体进行能量最小化。使用BIOVIA Discovery Studio Visualizer和PyMOL进行可视化。利用pkCSM和ProTox-II平台预测了顶击的ADMET特性。为了解决晶体结构中缺失的残基，使用AlphaFold2来预测全长蛋白质模型。采用GROMACS 2024.5软件包，利用AMBER-f99SB-ILDN力场、TIP3P水模型和120 mM NaCl浓度进行MD模拟。平衡是通过V-rescale和C-rescale恒温器实现的，然后是Parrinello-Rahman恒压器生产运行。MD轨迹分析包括RMSD、RMSF、Rg、SASA、h键和MM-PBSA，使用GROMACS工具，gmx_MMPBSA、VMD和MDAnalysis。图形抽象

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引用次数: 0

Quantum chemical study on the weak intermolecular interaction between 3,4-bis(3-nitrofurazan-4-yl) furoxan (DNTF) and microcrystalline wax 3,4-二（3-硝基呋喃赞-4-基）呋喃嘧啶（DNTF）与微晶蜡弱分子间相互作用的量子化学研究

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-04 DOI: 10.1007/s00894-025-06512-7

Jianfei Xu, Zhiwei Han, Yaning Li, Yuanlin Fan, Jianing Zhang

Context

Compatibility is a key factor restricting the engineering applications of 3,4-Bis(3-nitrofurazan-4-yl) furoxan (DNTF). To establish a scientific criterion for the compatibility of DNTF with other substances, this study uses the DNTF/WAX system as the research subject. By applying computational chemistry methods, it reveals the interactions and incompatibility mechanism between DNTF andMicrocrystalline Wax (MW). Molecular surface electrostatic potential studies indicate that electrostatic interactions exist between the side of DNTF away from the oxygen atom on the furazan ring and the side of MW containing alcoholic hydroxyl groups. IGMH analysis further reveals that these weak interactions consist of hydrogen bonding and van der Waals forces. AIM calculations reveal that the weak interactions at the bond critical points (BCPs) in the DNTF/MW system are primarily "weak"-level hydrogen bonds of the N···H-O type and hydrogen-bond-like interactions of the O···H-C type. Frontier molecular orbital (FMO) analysis reveals that compared with pure DNTF, the molecular orbital energy level difference ΔE of the DNTF/MW composite structure decreases by 21%. This indicates enhanced reactivity of the composite structure. Mayer bond order analysis verifies the accuracy of the FMO results: in the DNTF/MW composite structure, the bond orders of both the key pyrolysis initiation bond (O6-N3) and secondary initiation bonds decrease to varying degrees compared to the single-component DNTF. This study provides a theoretical basis for screening DNTF-based mixed explosive formulations and helps improve the safety of DNTF in practical applications.

Methods

The initial molecular structures of DNTF and MW used in this study were retrieved from the Cambridge Crystallographic Data Centre (CCDC) and optimized using Gaussian16 software at the B3LYP-D3/6-311G(d,p) computational level. To obtain the optimal bimolecular conformations of DNTF and MW, a conformational search method was employed: first, the Genmer package was used to generate 500 bimolecular configurations of DNTF/MW composites; then, the Molclus program was employed to invoke XTB software for structural optimization at the GFN2-xTB level, with five configurations of lower energy retained; subsequently, Gaussian16 software was called to perform optimization and frequency calculations for these structures at the B3LYP-D3(BJ)/6-31G* level; finally, the ORCA software was used to perform single-point energy calculations at the PWPB95-D3(BJ)/def2-TZVPP level for the structures optimized by Gaussian, thereby obtaining the free energy of each configuration, and the configuration with the lowest energy was selected based on the free energy for subsequent weak interaction analysis. Additionally, the counterpoise (CP) method was also used to correct for basis set superposition error (BSSE).

摘要相容性是制约3,4-二（3-硝基呋喃-4-基）呋喃嘧啶（DNTF）工程应用的关键因素。为了建立科学的DNTF与其他物质的相容性标准，本研究以DNTF/WAX体系为研究对象。应用计算化学方法，揭示了DNTF与微晶蜡（MW）的相互作用和不相容机理。分子表面静电势研究表明，在呋喃唑环上远离氧原子的DNTF一侧和含有醇羟基的MW一侧之间存在静电相互作用。IGMH分析进一步揭示了这些弱相互作用由氢键和范德华力组成。AIM计算结果表明，DNTF/MW体系在键临界点处的弱相互作用主要是N··h·O型的“弱”级氢键和O··h·c型的类氢键相互作用。前沿分子轨道（FMO）分析表明，与纯DNTF相比，DNTF/MW复合结构的分子轨道能级差ΔE减小了21%。这表明复合材料结构的反应性增强。Mayer键序分析验证了FMO结果的准确性：在DNTF/MW复合结构中，与单组分DNTF相比，关键热解引发键（O6-N3）和次级引发键的键序都有不同程度的降低。本研究为基于DNTF的混合炸药配方的筛选提供了理论依据，有助于提高DNTF在实际应用中的安全性。方法从剑桥晶体数据中心（Cambridge Crystallographic Data Centre， CCDC）获取DNTF和MW的初始分子结构，并在B3LYP-D3/6-311G（d,p）计算水平上使用Gaussian16软件进行优化。为了获得DNTF和MW的最佳双分子构型，采用构象搜索方法：首先，利用Genmer包生成500个DNTF/MW复合材料的双分子构型；然后，利用Molclus程序调用XTB软件在GFN2-xTB水平上进行结构优化，保留了5种较低能量的构型；随后，调用Gaussian16软件对这些结构进行B3LYP-D3(BJ)/6-31G*级的优化和频率计算；最后，利用ORCA软件对经过高斯优化的结构进行PWPB95-D3(BJ)/def2-TZVPP能级的单点能量计算，得到各构型的自由能，并根据自由能选择能量最低的构型进行后续的弱相互作用分析。此外，还利用平衡（CP）方法对基集叠加误差（BSSE）进行了校正。

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引用次数: 0

Multiscale theoretical study of infrared spectroscopy for the thermal denaturation process of aprotinin 抑肽蛋白热变性过程的红外光谱多尺度理论研究

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-04 DOI: 10.1007/s00894-025-06511-8

Wei Xiang, Jianjie Xu, Jianbo Hu, Tengxiao Guo, Yonggang Liu, Bingshuang Fan, Jia Wu, Hang Zhang, Yunfan Yang

Context

The stability of protein secondary structure is the basis for the realization of biological functions, and temperature induces conformational changes in proteins by disrupting the equilibrium of the internal hydrogen bond network. This study systematically elucidates the temperature-induced unfolding mechanism of aprotinin based on one-dimensional infrared spectroscopy (1D IR) and two-dimensional infrared spectroscopy (2D IR) simulated by molecular dynamics (MD) simulations. The simulations showed that the characteristic absorption peaks of the amide I band in the IR spectra of the aprotinin were blueshifted and weakened with increasing temperature, indicating that the hydrogen bond breaking leads to the secondary structure transformation of the aprotinin. The 2D IR simulations of aprotinin reveal that when the temperature rose to 333 K, the vibrational coupling peak of the β-sheet at (1625.4 cm⁻¹, 1653.4 cm⁻¹) disappears. At 353 K, new coupling peaks corresponding to random coil and β-turn appear at (1639.7 cm⁻¹, 1672.2 cm⁻¹), and these signals disappear at 373 K, indicating complete unfolding of aprotinin. During the heating process, the 2D IR spectral signal of the aprotinin shifted from excited-state absorption (ESA) to ground-state bleaching (GSB), reflecting the energy transfer process within the protein, and its dynamics process and spectral broadening rate were greatly affected by temperature. The unfolding pathway of aprotinin was again obtained by MD simulation and analyzed in comparison with infrared spectroscopy, and the unfolding behavior of the aprotinin was resolved at the atomic level.

Methods

In this work, the MD simulation of aprotinin was carried out by GROMACS, using the OPLS/AA force field and SPC/E water model, with a simulation duration of 500 ns and a time step of 2 fs. After the simulation, the C = O stretching vibrations of peptide bonds were extracted from the trajectory files to calculate the autocorrelation function and third-order nonlinear response function, which were Fourier transformed to obtain the 1D and 2D IR spectra of aprotinin. The DSSP program in GROMACS was used to quantitatively analyze the secondary structure content of aprotinin at various temperatures, and the conformational changes under different temperature conditions were visually analyzed by using VMD software.

蛋白质二级结构的稳定性是实现生物功能的基础，温度通过破坏蛋白质内部氢键网络的平衡引起蛋白质构象的变化。本研究基于一维红外光谱（1D IR）和分子动力学（MD）模拟的二维红外光谱（2D IR），系统地阐明了抑蛋白蛋白的温度诱导展开机制。模拟结果表明，随着温度的升高，抑肽蛋白红外光谱中酰胺I波段的特征吸收峰发生蓝移和减弱，表明氢键断裂导致抑肽蛋白二级结构转变。对抑肽蛋白的二维红外模拟表明，当温度升高到333 K时，β-片在（1625.4 cm−1,1653.4 cm−1）处的振动耦合峰消失。在353 K时，在（1639.7 cm−1,1672.2 cm−1）处出现了新的偶联峰，对应于随机线圈和β-turn，这些信号在373 K时消失，表明抑蛋白蛋白完全展开。在加热过程中，抑蛋白蛋白的二维红外光谱信号从激发态吸收（ESA）转变为基态漂白（GSB），反映了蛋白质内部的能量传递过程，其动力学过程和光谱展宽速率受温度影响较大。再次通过MD模拟得到抑蛋白蛋白的展开途径，并与红外光谱进行对比分析，在原子水平上解析抑蛋白蛋白的展开行为。方法采用GROMACS软件，采用OPLS/AA力场和SPC/E水模型，模拟时间为500 ns，时间步长为2 fs。仿真结束后，从轨迹文件中提取肽键的C = O伸缩振动，计算自相关函数和三阶非线性响应函数，对其进行傅里叶变换，得到抑肽蛋白的一维和二维红外光谱。利用GROMACS中的DSSP程序定量分析了抑蛋白蛋白在不同温度下的二级结构含量，并利用VMD软件直观分析了不同温度条件下的构象变化。

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引用次数: 0

Design and theoretical investigation of diphenylsulfone-based blue-emitting TADF materials for advanced OLED applications 基于二苯基砜的先进OLED蓝光TADF材料的设计与理论研究

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-03 DOI: 10.1007/s00894-025-06525-2

Bahjat S. Hameed, Faeq A. AL‑Temimei, Zainab S. Hussain

Context

This theoretical study addresses the challenge of creating efficient and stable blue-emitting materials for organic light-emitting diodes (OLEDs) by investigating a new series of diphenylsulfone (DPS) derivatives. The research focuses on designing compounds with favorable properties for thermally activated delayed fluorescence (TADF), a mechanism that allows for highly efficient light emission by utilizing both singlet and triplet excitons. The designed compounds demonstrate optimized singlet–triplet energy gaps ((Delta {E}_{ST})) ranging from 0.11 to 0.29 eV, which facilitates efficient reverse intersystem crossing (RISC). Simulations of their UV–Vis spectra show blue to bluish-green emission, with high photoluminescence quantum yields and peak wavelengths between 367 and 433 nm. Further analyses using electrostatic potential maps, a localized-orbital locator (LOL), and a reduced density gradient (RDG) confirm the electronic localization and non-covalent interactions essential for efficient TADF emission. The findings underscore the effectiveness of molecular design in tuning properties for advanced optoelectronic applications.

Methods

Density functional theory (DFT) and time-dependent DFT (TD-DFT) were used to explore the structural, electronic, and photophysical properties of the compounds. Ground-state geometries were optimized using the B3LYP/6-311G(d,p) level of theory in the gas phase. For accurate simulation of intermolecular charge transfer, excited-state calculations were performed with the CAM-B3LYP/6-311G(d,p) level. Computational analyses, including electrostatic potential, localized-orbital locator, and reduced density gradient, were conducted using the Gaussian 09 and Multiwfn 3.8 program suites. Molecular structures and properties were visualized with GaussView 5.0.8, while spectroscopic data were analyzed with Origin(Pro) 2024b.

本理论研究通过研究一系列新的二苯基砜（DPS）衍生物，解决了为有机发光二极管（oled）创造高效稳定的蓝色发光材料的挑战。该研究的重点是设计具有热激活延迟荧光（TADF）特性的化合物，这是一种利用单线态和三重态激子实现高效发光的机制。所设计的化合物具有优化的单重态-三重态能隙（(Delta {E}_{ST})），范围为0.11 ～ 0.29 eV，有利于高效的反向系统间交叉（RISC）。它们的紫外可见光谱模拟显示出蓝色到蓝绿色的发射，具有高的光致发光量子产率和峰值波长在367和433 nm之间。利用静电势图、定位轨道定位器（LOL）和降低密度梯度（RDG）的进一步分析证实了电子定位和非共价相互作用对于有效的TADF发射至关重要。这些发现强调了分子设计在先进光电应用中调谐特性的有效性。方法采用密度泛函理论（DFT）和时变DFT （TD-DFT）分析化合物的结构、电子和光物理性质。利用气相理论的B3LYP/6-311G（d,p）水平对基态几何形状进行了优化。为了精确模拟分子间电荷转移，在CAM-B3LYP/6-311G（d,p）水平上进行激发态计算。利用Gaussian 09和Multiwfn 3.8软件进行了静电势、定位轨道定位和密度梯度等计算分析。使用GaussView 5.0.8可视化分子结构和性质，使用Origin(Pro) 2024b分析光谱数据。

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引用次数: 0

DFT studies on the mechanism of one-pot α,γ-difunctionalization of β-ketoesters: regio-, chemo-, and stereoselectivity promoted by DBU/MeOH DFT研究了β-酮酯的一锅α，γ-二功能化机制：DBU/MeOH促进的区域选择性、化学选择性和立体选择性。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-01 DOI: 10.1007/s00894-025-06509-2

Ratiba Hadjadj Aoul, Abdelghani Adda, Hadjira Habib Zahmani, Moussa Sehailia, Stéphane Humbel

Context

1,3-Dicarbonyl derivatives, such as β-ketoesters, are inexpensive and readily available building blocks widely applied in organic synthesis for the preparation of bioactive molecules. Nevertheless, the mechanistic origins of their regio-, chemo-, and stereoselectivity in multicomponent transformations remain insufficiently understood. Here, the α,γ-difunctionalization of cyclic β-ketoesters with benzaldehyde, allyl bromide, DBU, and methanol was investigated via density functional theory (DFT) to elucidate these selectivities. The reaction follows a five-step mechanism comprising deprotonation, alkylation, γ-deprotonation, aldol condensation, and dehydration. Energetic analysis revealed that the initial deprotonation is kinetically favored through a bimolecular pathway (({Delta G}^{#}) = 8.35 kcal/mol), whereas alkylation occurs stereoselectively via the Si face and aldol condensation via the Re face. Methanol cooperates with DBU by stabilizing enolates through hydrogen bonding and lowering activation barriers. These insights rationalize the observed experimental selectivity and provide a theoretical framework for the rational design of new selective multicomponent reactions in organic synthesis.

Methods

All quantum chemical calculations were performed via Gaussian 16 at the B3LYP/6-31G(d,p) level of theory, with Grimme’s D3 dispersion correction. Transition states were confirmed by harmonic frequency analysis and connected to their reactants and products via intrinsic reaction coordinate (IRC) calculations. Solvent effects (THF) were modeled using the IEFPCM approach. Conceptual DFT descriptors were computed at the B3LYP/6-311++G(d,p) level to assess the electronic properties. Natural bond orbital (NBO) analysis was conducted with NBO. The topological features of the electron density were examined using Multiwfn (version 3.8) through QTAIM and IGMH analyses, and the molecular structures were visualized using VMD.

背景：1,3-二羰基衍生物，如β-酮酯，是一种廉价且易得的基础材料，广泛应用于有机合成中制备生物活性分子。然而，它们在多组分转化中的区域选择性、化学选择性和立体选择性的机制起源仍然没有得到充分的了解。本文通过密度泛函理论（DFT）研究了环β-酮酯与苯甲醛、烯丙基溴、DBU和甲醇的α，γ-双官能化反应，以阐明这些选择性。该反应分为去质子化、烷基化、γ-去质子化、醛醇缩合和脱水五步。动力学分析表明，初始去质子化反应倾向于双分子途径（Δ g# = 8.35 kcal/mol），而烷基化反应通过Si面立体选择性发生，醛醇缩聚通过Re面立体选择性发生。甲醇与DBU的协同作用是通过氢键稳定烯醇化物和降低活化障碍。这些发现合理化了观察到的实验选择性，并为有机合成中新的选择性多组分反应的合理设计提供了理论框架。方法：所有量子化学计算均采用高斯16在B3LYP/6-31G（d,p）理论水平上进行，并进行grime 's D3色散校正。通过谐波频率分析确定过渡态，并通过本征反应坐标（IRC）计算将过渡态与它们的反应物和生成物联系起来。采用IEFPCM方法模拟了溶剂效应（THF）。在B3LYP/6-311++G（d,p）水平上计算概念DFT描述符以评估电子性质。用自然键轨道（NBO）进行了分析。利用Multiwfn（3.8）软件通过QTAIM和IGMH分析检测了电子密度的拓扑特征，并利用VMD对分子结构进行了可视化。

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引用次数: 0

Tuning the photophysical properties of triphenylamine pyrazine-based dyes: role of π-spacers in DSSCs with iodine and copper-based redox shuttle 三苯胺吡啶基染料光物理性质的调整：π-间隔剂在碘和铜基氧化还原穿梭DSSCs中的作用。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-09-30 DOI: 10.1007/s00894-025-06507-4

Asha, Sumit Sahil Malhotra, Sunita Srivastava, Manoj Kumar Gangwar, Ranjan Kumar Mohapatra, Manoj Kumar Gupta, Azaj Ansari

Context

A series of donor-π-acceptor dyes were designed based on the structure of the experimentally reported TPP dye, which incorporates Triphenylamine (TPA) as the donor, Pyrazine as the π-bridge, and a carboxylic acid group as the acceptor. To enhance the photovoltaic performance of dye-sensitized solar cells, five new dyes (TPP1-TPP5) were modelled by introducing different alterations to the π-conjugated bridge. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations were carried out to examine how the alteration in the π-spacer influences the optical, electronic, and photovoltaic performance. All dyes displayed negative Gibbs free energy values for electron injection into TiO₂, confirming the thermodynamic favourability of the charge transfer process. Short-circuit current density (J_SC) was found as the highest for TPP3 and TPP4, outperforming the other TPP dyes with 1.40 mA cm⁻² and 1.87 mA cm⁻². Furthermore, with the lowest dye regeneration of ΔG_reg = 0.46 eV and a comparable open circuit voltage (V_oc) of 1.17 eV, TPA4 demonstrated higher regeneration kinetics. Natural bond order analysis was conducted to assess the bond strength and examine the molecular orbitals associated with the donor, π-spacer and acceptor unit. All the modelled dyes found strong non-linear optical characteristics having the linear polarizability (α) amplitudes greater than the first-order total polarizability (β_total) relative to the experimental dye. Light harvesting efficiency of the modelled dye TPP4 was found the maximum (89%) among the studied dyes. These findings show that π-spacer alteration is an effective strategy for improving overall dye performance in DSSCs.

Methods

Optimization of all species by using Gaussian16 with functional B3LYP and basis set 6-311G (d,p). NBO analysis was performed to explore the interactions between the filled orbitals of one part and the vacant orbitals of another part. TDDFT studies were performed using ORCA4.2 with Zeroth-Order Regular Approximation for accounting relativistic effects to calculate excitation energies.

背景：在实验报道的TPP染料结构的基础上，设计了一系列以三苯胺（TPA）为给体，吡嗪为π桥，羧酸基为受体的给体-π-受体染料。为了提高染料敏化太阳能电池的光电性能，对5种新型染料（TPP1-TPP5）的π共轭桥进行了模拟。采用密度泛函理论（DFT）和时变DFT （TDDFT）计算了π-间隔层的变化对光学、电子和光电性能的影响。所有染料都显示出负的吉布斯自由能值，证实了电荷转移过程的热力学优势。TPP3和TPP4的短路电流密度最高，分别为1.40 mA cm-2和1.87 mA cm-2。此外，TPA4的最低染料再生率为ΔGreg = 0.46 eV，开路电压（Voc）为1.17 eV，表现出较高的再生动力学。通过自然键序分析来评估键强度，并考察了与供体、π-间隔和受体单位相关的分子轨道。所有模拟染料均具有较强的非线性光学特性，其线性极化率（α）幅度大于实验染料的一阶总极化率（β总）。模拟染料TPP4的光收集效率最高（89%）。这些发现表明π-间隔层改变是提高DSSCs染料整体性能的有效策略。方法：利用具有B3LYP功能的Gaussian16和基集6-311G （d,p）对所有物种进行优化。通过NBO分析，探讨了其中一部分的填充轨道与另一部分的空轨道之间的相互作用。使用ORCA4.2进行TDDFT研究，并使用零阶正则逼近来计算相对论效应以计算激发能。

{"title":"Tuning the photophysical properties of triphenylamine pyrazine-based dyes: role of π-spacers in DSSCs with iodine and copper-based redox shuttle","authors":"Asha, Sumit Sahil Malhotra, Sunita Srivastava, Manoj Kumar Gangwar, Ranjan Kumar Mohapatra, Manoj Kumar Gupta, Azaj Ansari","doi":"10.1007/s00894-025-06507-4","DOIUrl":"10.1007/s00894-025-06507-4","url":null,"abstract":"<div><h3>Context</h3><p>A series of donor-π-acceptor dyes were designed based on the structure of the experimentally reported TPP dye, which incorporates Triphenylamine (TPA) as the donor, Pyrazine as the π-bridge, and a carboxylic acid group as the acceptor. To enhance the photovoltaic performance of dye-sensitized solar cells, five new dyes (TPP1-TPP5) were modelled by introducing different alterations to the π-conjugated bridge. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations were carried out to examine how the alteration in the π-spacer influences the optical, electronic, and photovoltaic performance. All dyes displayed negative Gibbs free energy values for electron injection into TiO<sub>2</sub>, confirming the thermodynamic favourability of the charge transfer process. Short-circuit current density (J<sub>SC</sub>) was found as the highest for TPP3 and TPP4, outperforming the other TPP dyes with 1.40 mA cm<sup>−2</sup> and 1.87 mA cm<sup>−2</sup>. Furthermore, with the lowest dye regeneration of ΔG<sub>reg</sub> = 0.46 eV and a comparable open circuit voltage (V<sub>oc</sub>) of 1.17 eV, TPA4 demonstrated higher regeneration kinetics. Natural bond order analysis was conducted to assess the bond strength and examine the molecular orbitals associated with the donor, π-spacer and acceptor unit. All the modelled dyes found strong non-linear optical characteristics having the linear polarizability (α) amplitudes greater than the first-order total polarizability (β<sub>total</sub>) relative to the experimental dye. Light harvesting efficiency of the modelled dye TPP4 was found the maximum (89%) among the studied dyes. These findings show that π-spacer alteration is an effective strategy for improving overall dye performance in DSSCs.</p><h3>Methods</h3><p>Optimization of all species by using Gaussian16 with functional B3LYP and basis set 6-311G (d,p). NBO analysis was performed to explore the interactions between the filled orbitals of one part and the vacant orbitals of another part. TDDFT studies were performed using ORCA4.2 with Zeroth-Order Regular Approximation for accounting relativistic effects to calculate excitation energies.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 10","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197825","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

Nitrogen-rich prismane-based cage compounds: impact of pentazole substitution on detonation and explosive performance 富氮棱镜基笼型化合物：戊唑取代对爆轰和爆炸性能的影响。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-09-26 DOI: 10.1007/s00894-025-06494-6

Anjali Sharma, Dhruba Kshetrimayum, Usman Muhammad Aliyu, Mridula Guin

Context

This research explores the impact of systematic addition of pentazole group on the explosive properties of prismane-based compounds on hexanitroprismane and hexaminoprismane. Replacing the NO₂ and NH₂ groups with N₅ in prismane cage-based molecules enhances the material’s energy density and stability, leading to more powerful and stable explosives. The structure-property relationship of the designed molecules is studied using DFT approach. These cage-based compounds exhibit potential as high-energy density explosive compounds reaching up to the level of CL20. Systematic addition of pentazole ring in the prismane cage improves stability and heat of formation. Functionalizing prismane with one pentazole ring can improve the HOF by 300 to 400 kJmol⁻¹. The impact of the number of pentazole rings on density is opposite in nature in -NO₂ and -NH₂ containing sets of molecules. The same trend is observed in the values of D, P, and Q of both sets of molecules as the number of pentazole group increased in the prismane. Insertion of a single pentazole ring in prismane for the nitro group substituted molecules has a better impact on improving the impact sensitivity. Pentazole group substitution enhances the energetic properties of prismane-based high energy density compounds, offering a promising avenue for the development of novel, high-performance explosives with tailored detonation characteristics.

Methods

Density functional theory (DFT) using Gaussian 16 software was used for all quantum chemical calculations. The optimization of the geometry of the designed compounds is performed at two different levels, e.g., B3LYP/6–311 + + G(d,p) and B3PW91/6-31G(d,p). Molecular surface and other properties are visualized using GaussView 6.0 software. The heat of formation (HOF) of the molecules is estimated using isodesmic reactions. The multiwfn program was used for the calculation of molecular surface properties.

背景：本研究探讨了系统加成戊唑基团对棱柱烷类化合物对己硝基棱柱烷和六检棱柱烷爆炸性能的影响。用N5取代棱柱笼基分子中的NO2和NH2基团，提高了材料的能量密度和稳定性，从而产生更强大、更稳定的炸药。利用DFT方法研究了设计分子的结构-性质关系。这些笼基化合物表现出作为高能量密度爆炸性化合物的潜力，达到CL20的水平。在棱柱笼中系统添加戊唑环，提高了稳定性和生成热。带一个戊唑环的功能化棱柱体可使HOF提高300 ~ 400 kmol -1。在含-NO2和-NH2的分子组中，戊唑环数对密度的影响性质相反。两组分子的D、P、Q值随正棱柱体中戊唑基团数目的增加呈相同的变化趋势。在棱柱体中为硝基取代分子插入单个戊唑环对提高冲击灵敏度有较好的效果。戊唑基取代提高了棱柱烷基高能量密度化合物的能量特性，为开发具有定制爆轰特性的新型高性能炸药提供了一条有希望的途径。方法：所有量子化学计算均采用高斯16软件的密度泛函理论（DFT）。设计的化合物在两个不同的水平上进行几何优化，例如B3LYP/6-311 + + G（d,p）和B3PW91/6-31G（d,p）。利用GaussView 6.0软件对分子表面及其他性质进行可视化。分子的生成热（HOF）是用等温反应来估计的。利用multiwfn程序计算分子表面性质。

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引用次数: 0

First-principles study on the influence of tensile deformation on the optoelectronic properties of the F-HfSe₂ system 拉伸变形对F-HfSe 2体系光电性能影响的第一性原理研究。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-09-25 DOI: 10.1007/s00894-025-06504-7

Tong Yuan, Guili Liu, Guoying Zhang

Context

Within the framework of first-principles density functional theory, this study investigates the impacts of doping and tensile deformation on the electronic and optical properties of HfSe₂. The research reveals that, after being doped with halogen elements, HfSe₂ undergoes a transition from a semiconductor to a metal, enhancing the electrical conductivity of the X-HfSe₂ systems (where X represents F, Cl, Br, or I). Among them, F-HfSe₂ exhibits the lowest formation energy and is thus selected as the research object for tensile deformation studies. The study demonstrates that, as the tensile strain increases, the energy band values of F-HfSe₂ increase linearly, enabling effective regulation of its band structure. The density of states indicates that the main contributions come from the 6d orbitals of Hf and the 4p orbitals of Se, with the F atoms contributing minimally. F atoms primarily regulate the energy bands through charge transfer processes. Optically, tensile strain enhances the light-absorbing capacity of F-HfSe₂ and induces a redshift, making it applicable in the visible and near-infrared ranges. This is attributed to the bandgap changes caused by tensile deformation. Consequently, F-HfSe₂ holds promise as an ideal material for photodetectors.

Methods

Utilizing the CASTEP module within Materials Studio software under the framework of first-principles density functional theory (DFT), geometric optimizations and optoelectronic structure calculations were performed for both intrinsic HfSe₂ and doped systems. The GGA-PBE functional was chosen for its computational efficiency and the consistency of its calculated band structure trends with more precise HSE methods, despite its tendency to underestimate bandgaps. But rigorous convergence tests were conducted to ensure the precision and reliability of the results. Specifically, a 7 × 7 × 1 K-point grid was selected for Brillouin Zone sampling after repeated testing, and the plane-wave cutoff energy was set at 600 eV. Energy convergence per atom was set at 1.0 × 10⁻⁵ eV, force convergence at 0.03 eV/Å, with stress and displacement limits at 0.05 GPa and 0.01 Å, respectively. A vacuum spacing of 20 Å was implemented to prevent interactions between periodically replicated units.

背景：本研究在第一性原理密度泛函理论的框架下，研究了掺杂和拉伸变形对HfSe₂的电子和光学性质的影响。研究表明，在掺杂卤素元素后，HfSe₂经历了从半导体到金属的转变，增强了X-HfSe₂体系的导电性（其中X代表F， Cl， Br或I）。其中，F-HfSe₂的地层能量最低，因此被选为拉伸变形研究的研究对象。研究表明，随着拉伸应变的增加，F-HfSe 2的能带值线性增加，可以有效调节其能带结构。态密度表明Hf的6d轨道和Se的4p轨道是主要的贡献源，其中F原子的贡献最小。F原子主要通过电荷转移过程调节能带。在光学上，拉伸应变增强了F-HfSe 2的光吸收能力，并引起红移，使其适用于可见光和近红外范围。这是由于拉伸变形引起的带隙变化。因此，F-HfSe 2有望成为光电探测器的理想材料。方法：利用Materials Studio软件中的CASTEP模块，在第一性原理密度泛函理论（DFT）的框架下，对本态和掺杂体系进行几何优化和光电子结构计算。之所以选择GGA-PBE泛函，是因为它的计算效率高，而且与更精确的HSE方法计算出的能带结构趋势一致，尽管它倾向于低估带隙。但为了保证结果的准确性和可靠性，进行了严格的收敛测试。其中，经过反复测试，选取7 × 7 × 1 k点网格进行布里渊区采样，将平面波截止能量设置为600 eV。每个原子的能量收敛为1.0 × 10 eV，力收敛为0.03 eV/Å，应力和位移极限分别为0.05 GPa和0.01 Å。真空间隔为20 Å，以防止周期性复制单元之间的相互作用。

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引用次数: 0

Machine-learned density functional based quantum chemical computations for ethane: performance of DeepMind 21 on potential energy surface and molecular properties 基于机器学习密度泛函的乙烷量子化学计算：DeepMind 21在势能表面和分子性质上的表现。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-09-25 DOI: 10.1007/s00894-025-06451-3

B. Jijila, S. Susannal Ezhilarasi, V. Nirmala

Context

Machine learning (ML) has proven to be a promising method in quantum chemistry calculations. Researchers at Google DeepMind established the superior performance of a machine-learned functional DeepMind 21 (DM21), the neural network-based functionals which emerged as a powerful tool for developing exchange–correlation energy approximation in density functional theory (DFT), to accurately explain the charge delocalization and strong correlation. While many researchers have cited the work of DeepMind, still there remains a paucity of research publications that perform algorithmic computations with DeepMind’s AI model for quantum sciences. To address this lacuna, this paper investigates quantum chemistry algorithmic computations of potential energy surface and analysis properties of ethane molecule (C₂H₆) by employing the machine learning model to predict exchange–correlation potential. This paper utilizes neural density functional, DeepMind 21 to compute the dipole moment, molecular orbitals (HOMO/LUMO), and long-range interactions. Our computations were based on DM21m TensorFlow neural network model-based prediction of exchange–correlation potential, and then using this prediction to compute self-consistent field energies using PySCF Python package with cc-pVDZ Dunning dual basis set. The accuracy of the DM21 functional was rigorously assessed through comparison with conventional DFT methods (B3LYP, PW6B95) and the reference CCSD(T) standard. The findings indicate that the DM21 functional yields result in close agreement with the CCSD(T) benchmark energies and established literature values, confirming its efficacy for PES generation and quantum chemical computation in systems like ethane. This investigation demonstrates the suitability of the deep learning density functional for quantum science computations of ethane molecule for the first time.

Methods

In this method, the potential energy surfaces and properties (dipole moment, molecular orbitals) are computed using machine-learned density function approximation using pretrained deep learning models provided by DeepMind 21 researchers. By inserting deep learning inference in density functional theory (DFT) with a pretrained neural network, self-consistent field (SCF) energy at different geometries along the coordinate of interest is computed, and hence potential energy surfaces are computed and obtained. For a given specified molecular geometry, the algorithm computes the electron density vector, which is then used as a machine learning feature input for a pretrained DM21 deep learning model to predict the exchange–correlation. This methodology was implemented in a Python source code using frameworks such as PySCF and DM21.

背景：机器学习（ML）已被证明是量子化学计算中一种很有前途的方法。b谷歌DeepMind的研究人员建立了机器学习功能DeepMind 21 （DM21）的卓越性能，基于神经网络的功能成为密度泛函理论（DFT）中发展交换相关能量近似的强大工具，以准确解释电荷离域和强相关性。虽然许多研究人员引用了DeepMind的工作，但仍然缺乏用DeepMind的量子科学人工智能模型进行算法计算的研究出版物。针对这一不足，本文利用机器学习模型预测交换相关势，研究了乙烷分子（C2H6）势能面的量子化学算法计算和分析性质。本文利用神经密度函数、DeepMind 21计算偶极矩、分子轨道（HOMO/LUMO）和远程相互作用。我们的计算是基于DM21m TensorFlow神经网络模型预测交换相关势，然后使用PySCF Python包与cc-pVDZ Dunning对偶基集计算自洽场能。通过与传统DFT方法（B3LYP, PW6B95）和参考CCSD(T)标准进行比较，严格评估DM21泛函的准确性。研究结果表明，DM21的功能产率与CCSD(T)基准能量和已建立的文献值非常接近，证实了其在乙烷等体系中PES生成和量子化学计算中的有效性。该研究首次证明了深度学习密度泛函在乙烷分子量子科学计算中的适用性。方法：在该方法中，利用DeepMind 21研究人员提供的预训练深度学习模型，使用机器学习密度函数近似计算势能表面和性质（偶极矩，分子轨道）。通过在密度泛函理论（DFT）中插入深度学习推理和预训练神经网络，计算出沿感兴趣坐标的不同几何形状上的自洽场（SCF）能量，从而计算得到势能面。对于给定的特定分子几何形状，该算法计算电子密度矢量，然后将其用作预训练的DM21深度学习模型的机器学习特征输入，以预测交换相关性。该方法是在Python源代码中使用PySCF和DM21等框架实现的。

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引用次数: 0