Journal of Molecular Modeling最新文献_第7页

Kinetics of hydrogen migration and string of conformation transformation for pyruvic acid dimer under external electric field 外加电场作用下丙酮酸二聚体氢迁移和构象链转变动力学

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-11-06 DOI: 10.1007/s00894-025-06560-z

Rui-zhi Feng, Xiao-jiang Li, Ai-chuan Liu, Jian Kuo, Su-rong Yan, Wei Zhang

Context

To reveal the biochemical mechanism of pyruvic acid under the bioelectric currents, the effect of the external electric field on the intermolecular double-proton cooperativity migration was investigated for the dimer, accompanied by a comparison of the conformation transformation. The results indicate that the influences of the external electric fields on the transition state of the proton migration, i.e., the changes in the molecular structures, atoms in molecules, surface electrostatic potentials, and potential barriers, are closely related to the directions of the fields. The spatial order parameters of the conformation transformation of pyruvic acid can be quickly converged through the umbrella sampling and parameter averaging, thereby obtaining the potential energy surface of the potential of mean force. Under the strong external electric field, the barrier heights of the double-proton cooperativity migration are close to the free energy change of the conformation transformation, indicating the competition between the proton cooperativity transfer and conformation transformation. This study is of importance for revealing furthermore the essence of the competition between the proton migration and conformation transformation of the biomolecules stimulated by the bioelectric currents.

Methods

The effects of external electric fields on the double-proton cooperativity migration reaction pathway, potential barrier, and rate constant of the pyruvic acid dimer were studied using the M06-2X/6-311++G**, M06-2X/aug-cc-pVTZ, and CCSD(T)/6-311++G(2d,p) methods by using Gaussian 09 packages. A chaotic finite temperature string model with enhanced sampling for molecular conformation transformation was constructed, and the free energy change of conformation transformation under external electric field was studied by the finite temperature string (FTS) method with the CHARMM22 force field from NAMD software packages and PLUMED program.

为了揭示生物电流作用下丙酮酸的生化机制，研究了外加电场对二聚体分子间双质子协同迁移的影响，并比较了构象转变。结果表明，外加电场对质子迁移过渡态的影响，即分子结构、分子内原子、表面静电势和势垒的变化，与电场方向密切相关。通过伞式采样和参数平均，可以快速收敛丙酮酸构象变换的空间阶参量，从而得到平均力势的势能面。在强外电场下，双质子协同迁移的势垒高度与构象转变的自由能变化接近，表明质子协同迁移与构象转变之间存在竞争关系。本研究对于进一步揭示生物电流刺激下质子迁移与生物分子构象转化竞争的本质具有重要意义。方法采用高斯09封装，采用M06-2X/6-311++G**、M06-2X/aug-cc-pVTZ和CCSD(T)/6-311++G（2d,p）方法研究了外加电场对丙酮酸二聚体双质子协同迁移反应途径、势垒和速率常数的影响。建立了增强采样的分子构象变换混沌有限温度串模型，利用NAMD软件和PLUMED程序中的CHARMM22力场，采用有限温度串（FTS）方法研究了外电场下分子构象变换的自由能变化。

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引用次数: 0

Strain regulation of the optoelectronic characteristics of arsenene/PtSeS heterostructure: promoting smart diagnosis 砷/PtSeS异质结构光电特性的应变调节：促进智能诊断。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-29 DOI: 10.1007/s00894-025-06548-9

Lisha Lin, Jing Li

Context

The advancement of novel sensing materials significantly enhances the precision of early disease diagnosis and treatment. This study focuses on the fabrication of nano-sensing materials, specifically Janus arsenene/PtSeS (stacking-I and stacking-II), and examines their performance in strain sensing. The calculation results indicate that both stacking configurations exhibit excellent thermodynamic stability, with formation energies of − 3.27 eV and − 3.35 eV, respectively. Electronic structure analysis shows that both are indirect bandgap semiconductors, with bandgap values of 1.229 eV and 0.845 eV, respectively, and charge transfer occurs at the interface (net transfer amounts of 0.26 |e| and 0.28 |e|, respectively). Under applied tensile or compressive strain, ranging from 0 to 4%, the bandgaps of both heterojunctions exhibit a gradual decrease or increase. In the visible light spectrum, the absorption coefficient of the heterojunctions approaches approximately 1.6 × 10⁵ cm⁻¹. These research outcomes are expected to facilitate the integration of these materials into medical diagnostic devices, including endoscopes.

Methods

All density functional theory calculations were conducted utilizing the CASTEP software package. The electron–electron exchange interaction was addressed through the Perdew-Burke-Ernzerhof functional, which operates within the framework of the generalized gradient approximation. To mitigate the known issue of band gap underestimation associated with the PBE functional, the Heyd-Scuseria-Ernzerhof hybrid functional was employed to enhance the electronic structure and optical absorption properties of the arsenene/PtSeS heterojunction.

背景：新型传感材料的进步显著提高了疾病早期诊断和治疗的精度。本研究重点研究了纳米传感材料的制备，特别是Janus arsenene/PtSeS (stacking-I和stacking-II)，并研究了它们在应变传感中的性能。计算结果表明，两种构型均表现出良好的热力学稳定性，形成能分别为- 3.27 eV和- 3.35 eV。电子结构分析表明，两者均为间接带隙半导体，带隙值分别为1.229 eV和0.845 eV，并在界面处发生电荷转移（净转移量分别为0.26 |e|和0.28 |e|）。在0 ~ 4%的拉伸或压缩应变范围内，两种异质结的带隙均呈逐渐减小或增大的趋势。在可见光光谱中，异质结的吸收系数接近1.6 × 105 cm-1。这些研究成果有望促进将这些材料整合到医疗诊断设备中，包括内窥镜。方法：采用CASTEP软件包进行密度泛函理论计算。电子-电子交换相互作用通过Perdew-Burke-Ernzerhof泛函处理，该泛函在广义梯度近似的框架内运行。为了解决已知的与PBE功能相关的带隙低估问题，采用Heyd-Scuseria-Ernzerhof杂化功能来增强砷/PtSeS异质结的电子结构和光学吸收性能。

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引用次数: 0

Using spin–orbit DFT module (SODFT) in indium compounds: enthalpies of formation and bond dissociation 在铟化合物中使用自旋轨道DFT模块（SODFT）：生成焓和键解离。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-28 DOI: 10.1007/s00894-025-06519-0

Cleuton de Souza Silva

Context

The indium compounds were investigated both with and without spin–orbit correction, which highlighted the importance of this correction for indium compounds. The methods used in this work showed good results for enthalpy of formation when compared with other experimental results and studies in the literature with CCSD(T)/CBS. However, for bond dissociation, the results of the studied methods were highly divergent and not considered very effective when compared with experimental data from the literature. Notably, the G4-T-V2, G4-T-V3, and G4-T-V4 methods demonstrated good results for enthalpy of formation. These methods are particularly noteworthy because they utilise three energy coefficient adjustments and do not rely on higher-level correction.

Methods

We used the G4MP2-XK method along with 30 other composite methods developed by Martin and Semidalas.

背景：对铟化合物进行了有和没有自旋轨道校正的研究，强调了这种校正对铟化合物的重要性。用CCSD(T)/CBS与其他实验结果和文献研究相比，本文所采用的方法得到了较好的生成焓结果。然而，对于键解离，研究方法的结果分歧很大，与文献中的实验数据相比，并不是很有效。值得注意的是，G4-T-V2、G4-T-V3和G4-T-V4方法对生成焓有较好的测定结果。这些方法特别值得注意，因为它们利用三种能量系数调整，而不依赖于更高级别的校正。方法：采用G4MP2-XK方法以及Martin和Semidalas开发的其他30种复合方法。

引用次数: 0

Detailed investigation of the spectroscopic features of nicardipine hydrochloride using experimental and quantum chemical methods 用实验和量子化学方法详细研究了盐酸尼卡地平的光谱特征。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-28 DOI: 10.1007/s00894-025-06539-w

Sumeyra Can, Mehmet Cinar, Ozlem Baris

Context

The structural and spectroscopic properties of drug groups can be determined using spectroscopic techniques and quantum chemical calculations. In this study, the structural and spectroscopic properties of nicardipine, a potent calcium channel blocker belonging to the dihydropyridine drug group, were investigated. For this purpose, FT-IR, Raman, NMR, and UV–Vis spectra of nicardipine hydrochloride were recorded. The ground state geometry optimization performed under vacuum conditions showed excellent agreement with X-ray diffraction (XRD) data, with root-mean-square deviations of bond lengths and bond angles calculated as 0.017 Å and 2.2°, respectively. Vibrational spectrum analysis revealed all characteristic modes, and theoretical B3LYP predictions largely agreed with experimental data. NMR spectra recorded in chloroform solvent confirmed the molecular structure of nicardipine. A comparison with previously reported data revealed significant differences in the proton NMR results, while the carbon NMR data showed consistency. The gauge-invariant atomic orbital (GIAO) method, commonly used for NMR spectrum prediction, yielded results within an acceptable error range despite minor inconsistencies arising from differences between experimental and computational conditions. In the UV–Vis spectrum of nicardipine HCl, an absorption peak corresponding to π-π* excitation was observed at 238 nm.

Method

The geometric optimizations and vibration spectra of the nicardipine drug molecule were performed using the Gaussian 09 program with the B3LYP functional and the 6–311 + + G(d,p) basis set. Visualizations were performed using the GaussView 5.0 interface program. NMR spectra were recorded in chloroform solvent using the GIAO method. Molecular electrostatic potential (MEP) maps and Mulliken atomic charges were analyzed to gain deeper insight into the electronic properties.

背景：利用光谱学技术和量子化学计算可以确定药物基团的结构和光谱性质。本研究对二氢吡啶类强效钙通道阻滞剂尼卡地平的结构和光谱性质进行了研究。为此，记录了盐酸尼卡地平的红外光谱、拉曼光谱、核磁共振光谱和紫外可见光谱。在真空条件下进行的基态几何优化与x射线衍射（XRD）数据吻合良好，键长和键角的均方根偏差分别为0.017 Å和2.2°。振动谱分析揭示了所有的特征模式，理论B3LYP预测与实验数据基本一致。在氯仿溶剂中记录的核磁共振光谱证实了尼卡地平的分子结构。与先前报道的数据进行比较，发现质子核磁共振结果存在显着差异，而碳核磁共振数据显示一致性。通常用于核磁共振谱预测的测量不变原子轨道（GIAO）方法，尽管实验和计算条件之间的差异引起了轻微的不一致，但其结果在可接受的误差范围内。在盐酸尼卡地平的紫外可见光谱中，在238 nm处出现π-π*激发的吸收峰。方法：采用高斯09程序，以B3LYP泛函和6-311 + + G（d,p）基集对尼卡地平药物分子进行几何优化和振动谱分析。使用GaussView 5.0接口程序进行可视化。用GIAO法在氯仿溶剂中记录核磁共振波谱。分析了分子静电势（MEP）图和Mulliken原子电荷，以更深入地了解电子性质。

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引用次数: 0

Surface interactions and radical generation in TCD decomposition: a DFT approach TCD分解中的表面相互作用和自由基生成：DFT方法。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-27 DOI: 10.1007/s00894-025-06545-y

Samantha E. Knoth, Daniel Tunega, Adelia J. A. Aquino

Context

Exo-tetrahydrodicyclopentadiene (exo-TCD) is a key component of Jet Propellant-10 (JP-10), a high-density hydrocarbon fuel extensively used in aerospace applications. The addition of aluminum particles enhances fuel performance and reactivity, making the understanding of initial decomposition pathways crucial. This study used density functional theory (DFT) calculations to investigate the initial hydrogen abstraction reactions in the decomposition of exo-TCD, with emphasis on radical formation processes. A significant aspect of this work is the role of the γ-Al₂O₃ surface in facilitating these reaction pathways, especially considering surface defects modeled by removing hydrogen from active hydroxyl groups. Five known active hydroxyl sites on γ-Al₂O₃ (A_Ia, A_Ib, A_IIA, B_IIb, and B_III) were used to construct complexes with exo-TCD. The formed complexes are primarily van der Waals interactions, with energies ranging from −11 to −20 kcal/mol and no substantial energy differences between configurations. The results indicate that hydrogen abstraction from the R4 site of exo-TCD is the most energetically favorable, owing to the molecular structure. Surface defects can boost reactivity by facilitating hydrogen abstraction, as seen in spontaneous H transfer to the active A_Ib site and low energetic barrier to the transition state of the H-abstraction of the B_IIb site. These findings improve the understanding of TCD decomposition and the catalytic role of γ-Al₂O₃, aiding the development of better propulsion fuels and energetic materials.

Methods

The calculations used the Perdew–Burke–Ernzerhof PBE exchange–correlation functional with split-valence polarization (SVP) and triple-zeta valence polarization (TZVP) basis sets, combined with the resolution of identity (RI) method to accelerate four-center electron repulsion integrals. The PBE results were benchmarked with the hybrid meta-GGA functional M06-2X. Dispersion correction D3 was applied throughout. All computations were performed using the Turbomole program.

外展四氢二环戊二烯（exo-TCD）是喷气推进剂-10 （JP-10）的关键成分，JP-10是一种广泛应用于航空航天领域的高密度碳氢燃料。铝颗粒的添加提高了燃料的性能和反应性，使初始分解途径的理解至关重要。本研究利用密度泛函理论（DFT）计算研究了外型tcd分解过程中的初始吸氢反应，重点研究了自由基的形成过程。这项工作的一个重要方面是γ-Al2O3表面在促进这些反应途径中的作用，特别是考虑到通过从活性羟基上去除氢来模拟的表面缺陷。利用γ-Al2O3上已知的5个活性羟基位点（A_Ia, A_Ib, A_IIA， B_IIb和B_III）与外显子tcd构建配合物。形成的配合物主要是范德华相互作用，能量范围在-11 ~ -20 kcal/mol之间，不同构型之间没有明显的能量差异。结果表明，由于分子结构的原因，从外置tcd的R4位点提取氢是最有利的。表面缺陷可以通过促进氢的提取来提高反应性，如自发的H转移到活性的A_Ib位点和B_IIb位点的H提取过渡态的低能垒。这些发现提高了对TCD分解和γ-Al2O3催化作用的认识，有助于开发更好的推进燃料和含能材料。方法：采用具有分裂价极化（SVP）和三价极化（TZVP）基集的Perdew-Burke-Ernzerhof PBE交换相关泛函进行计算，结合单位分辨率（RI）方法加速四中心电子排斥积分。PBE结果用混合meta-GGA功能M06-2X进行基准测试。色散校正D3贯穿始终。所有计算均使用Turbomole程序进行。

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引用次数: 0

Adsorption of H(_{2})S and SO(_{2}) in IRMOF-1: a computational study using DFT and GCMC simulations IRMOF-1对h2s和so2的吸附：基于DFT和GCMC模拟的计算研究

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-27 DOI: 10.1007/s00894-025-06533-2

Isaac O. M. Magalhães, Nailton Martins Rodrigues, Daniel F. Scalabrini Machado, José A. S. Laranjeira, Julio R. Sambrano, João B. L. Martins

Context

H(_{varvec{2}})S and SO(_{varvec{2}}) are harmful gases found in nature and from industrial production. This study investigated their adsorption within IRMOF-1 cavities by means of periodic density functional theory. QTAIM-based IGMH isosurface and adsorption energy analyses provided insight into the SO(_{varvec{2}}) (^{varvec{...}})H(_{varvec{2}})S interactions, where SO(_{varvec{2}}) is directed to the inorganic moiety. The mixed gases show significant interactions between SO(_{varvec{2}}) and H(_{varvec{2}})S. Regardless of the density functional approximation chosen, SO(_{varvec{2}}) exhibited a stronger adsorption preference over H(_{varvec{2}})S. B3LYP BSSE and dispersion-corrected interaction energies were consistently stronger than HSE06, whereas the B3LYP band gap presents larger values than HSE06. Grand Canonical Monte Carlo (GCMC) simulations further confirmed that SO(_{varvec{2}}) preferentially occupies the IRMOF-1 pores, with higher pressures enhancing adsorption.

Methods

Periodic optimizations were performed using the density functional approximations (DFAs) with B3LYP and HSE06 hybrid functionals, incorporating D3 dispersion and BSSE counterpoise corrections. Two basis sets were employed to analyze the B3LYP and HSE06 electronic and adsorption results: the pob-TZVP basis set and the modified m-6-311G(d) basis set. GCMC simulations were conducted to evaluate adsorption isotherms, while QTAIM and IGMH were used to account for the interaction behavior.

背景：h2s和so2是自然界和工业生产中发现的有害气体。利用周期密度泛函理论研究了它们在IRMOF-1腔内的吸附。基于qtaim的IGMH异质面和吸附能分析提供了对so2的深入了解。h2s相互作用，so2被导向无机部分。无论选择何种密度泛函近似，so2都表现出比h2s更强的吸附偏好，B3LYP的BSSE和色散校正的相互作用能始终比HSE06强，而B3LYP的带隙值则比HSE06大。大规范蒙特卡罗（GCMC）模拟进一步证实了so2优先占据IRMOF-1孔隙，较高的压力促进了吸附。方法：利用B3LYP和HSE06混合泛函的密度泛函近似（dfa）进行周期性优化，并结合D3色散和BSSE平衡校正。B3LYP和HSE06的电子和吸附结果采用两个基组进行分析：pob-TZVP基组和改性m-6-311G(d)基组。GCMC模拟用于评估吸附等温线，QTAIM和IGMH模拟用于解释相互作用行为。

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引用次数: 0

New considerations on the first steps for the conversion of chloromethane to olefins from a DFT perspective 从DFT角度对氯甲烷制烯烃第一步的新思考。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-27 DOI: 10.1007/s00894-025-06546-x

Anibal Sierraalta, Rafael Añez, David S. Coll

Context

This work investigates the initial stages of the reaction in the conversion of chloromethane to light olefins (CMTO) on NaZSM-5 zeolite. Density functional theory (DFT) calculations indicate that the overall reaction is endothermic in bulk but exothermic on the surface. The formation of the :CH₂ species is highly endothermic and has a high activation barrier. The migration of the CH₃ group between oxygen atoms within the zeolite structure is energetically less demanding than the formation of the :CH₂ species. Finally, the formation of ZOCH2CH3 from ZOCH3 + CH3Cl occurs through a two-step mechanism that includes a migration of the CH₃ group with energy barriers of +95.2 and +148.2 kJ mol⁻¹. The results obtained with ONIOM2 are qualitatively comparable to those obtained with VASP in terms of energy and geometry.

Method

DFT calculations were carried out using Gaussian 09 and VASP code. For cluster models, ONIOM2(DF:PM3) was used with the ωB97x-D, PBE, and M062X density functionals (DF) along with the relativistic Stevens effective core potential and its corresponding basis set. QST2, IRC, and frequency calculations are performed to characterize the transition states. For periodic calculations, structure optimization was carried out using the PBE functional with the D3 dispersion of Grimme, a plane-wave basis set, and the PAW representation of the atomic cores. The electronic structures of the systems were analyzed using PDOS.

背景：本文研究了在NaZSM-5分子筛上氯甲烷转化为轻烯烃（CMTO）反应的初始阶段。密度泛函理论（DFT）计算表明，整个反应总体上是吸热的，而表面是放热的。CH2的形成是高度吸热的，具有很高的活化屏障。沸石结构中，CH3基团在氧原子间的迁移在能量上比CH2基团的形成要求低。最后，ZOCH3 + CH3Cl通过两个步骤形成ZOCH2CH3，其中包括CH3基团的迁移，能垒为+95.2和+148.2 kJ mol-1。使用ONIOM2获得的结果在能量和几何形状方面与使用VASP获得的结果在质量上相当。方法：采用Gaussian 09和VASP代码进行DFT计算。对于聚类模型，使用ONIOM2（DF:PM3）与ωB97x-D、PBE和M062X密度泛函（DF）以及相对论性Stevens有效核心势及其相应的基集。执行QST2、IRC和频率计算来表征过渡状态。在周期性计算中，利用grime的D3色散、平面波基集和原子核心的PAW表示进行结构优化。利用PDOS分析了系统的电子结构。

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引用次数: 0

Stereochemical determination of hydroxylated derivatives of progesterone using DFT NMR calculations and DP4+ probability 用DFT核磁共振计算和DP4+概率立体化学测定孕酮羟基化衍生物。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-27 DOI: 10.1007/s00894-025-06547-w

Cassia R. Rambo, Samuel F. C. Paula, André L. M. Porto, Isac G. Rosset

Context

Hydroxylated derivatives of progesterone are biologically relevant compounds obtained through regio- and stereoselective biotransformations, but determining their stereochemical configuration is challenging due to subtle NMR chemical shift differences. In this study, monohydroxylated (prog-15-OH) and dihydroxylated (prog-7,15-di-OH) progesterone derivatives produced by Penicillium oxalicum CBMAI 1996 were analyzed. Quantum NMR calculations combined with statistical validation allowed the unambiguous identification of the 15β-OH and 7β,15β-di-OH isomers, with DP4+ probabilities of 100% and 99.8%, respectively. These findings confirm the stereochemical outcome of enzymatic hydroxylation and demonstrate the reliability of integrating computational NMR with experimental spectroscopy for resolving stereochemical ambiguities in complex steroidal frameworks.

Methods

Conformational searches were performed using the MMFF94 force field, followed by DFT geometry optimizations at the B3LYP/6-311G(2d,p) level with IEFPCM (chloroform). NMR shielding tensors were computed by the GIAO method at the mPW1PW91/6-311G(d,p) level with PCM (chloroform), and chemical shifts were referenced to TMS. Experimental and calculated ¹H/¹³C shifts were compared using correlation coefficients (R²), mean absolute deviation (MAD), root mean square deviation (RMSD), and DP4+ probability analysis. All calculations were performed with Gaussian 16.

背景：孕酮羟基化衍生物是通过区域和立体选择性生物转化获得的生物相关化合物，但由于细微的核磁共振化学位移差异，确定其立体化学构型具有挑战性。本研究对草酸青霉CBMAI 1996生产的单羟基（prog-15-OH）和二羟基（prog-7,15- dioh）黄体酮衍生物进行了分析。量子核磁共振计算与统计验证相结合，使15β-OH和7β，15β-二- oh异构体的DP4+概率分别为100%和99.8%。这些发现证实了酶促羟基化的立体化学结果，并证明了将计算核磁共振与实验光谱学结合起来解决复杂甾体框架中立体化学歧义的可靠性。方法：利用MMFF94力场进行构象搜索，然后用IEFPCM（氯仿）在B3LYP/6-311G（2d,p）水平上进行DFT几何优化。采用GIAO方法计算了PCM（氯仿）在mPW1PW91/6-311G（d,p）水平上的核磁共振屏蔽张量，并参考了TMS的化学位移。通过相关系数（R2）、平均绝对偏差（MAD）、均方根偏差（RMSD）和DP4+概率分析比较实验和计算的1H/13C位移。所有的计算都用高斯函数进行。

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引用次数: 0

Adsorption of explosive and hazardous compounds by cyclo[10]carbon and cyclo[14]carbon: A DFT study 环[10]碳和环[14]碳对爆炸性和有害化合物的吸附：DFT研究。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-27 DOI: 10.1007/s00894-025-06554-x

Qiong Wu, Zhihao Zheng, Siyang Cheng, Juan Xu, Zusheng Hang, Weihua Zhu

The adsorption and detection of explosive and hazardous compounds are highly important for preventing accidents. In this study, two new synthesized cyclo[n]carbons (n = 10, C₁₀. n = 14, C₁₄) were employed as new sensors to adsorb six explosive (N₃H, NH₂NO₂) or hazardous compounds (CO, HCHO, HCN, NH₃). Based on the DFT calculations, first of all, it is found that all six adsorbates are adsorbed inside the conjugated ring of of C₁₀ and C₁₄ with the adsorption energies ranged from 15.7 to 38.9 kJ/mol, showing the typical weak-to-moderate physical adsorption characteristic. Then, C₁₄ indicated the stronger adsorption toward six small molecules than C₁₀ in general. And, both C₁₀ and C₁₄ showed the best selectivity toward the adsorption of NH₂NO₂ than others. Plus, the adsorption mechanisms to the same adsorbate are different sometimes for two cyclo[n]carbons, due to the difference in the shape, size, and type of chemical bonds of them. Finally, the short recovery time ranged from 8.7 fs to 0.024 ms, and significant changes in the spectrum also supports the high potential for using C₁₀ and C₁₄ as sensors for adsorbing and detecting these six explosive or hazardous compounds.

All of the calculations on the structures were carried out by using the Gaussian 09 software at the M06-2X/6-311G(d,p), M06-2X-D3/6-311G(d,p), and M06-2X-D3/6-311++G(d,p) level. In addition, further calculations on the properties and interactions were performed by using the Multiwfn software.

爆炸性危险化合物的吸附和检测对于防止事故的发生具有重要意义。本研究合成了两个新的环[n]碳（n = 10, C10）。n = 14, C14)作为新型传感器可吸附6种炸药（N3H, NH2NO2）或有害化合物（CO， HCHO， HCN, NH3）。通过DFT计算，首先发现6种吸附剂均吸附在C10和C14的共轭环内，吸附能范围在15.7 ~ 38.9 kJ/mol之间，表现出典型的弱-中等物理吸附特征；C14对6个小分子的吸附能力总体上强于C10。C10和C14对NH2NO2的选择性较好。此外，由于两个环[n]碳的形状、大小和化学键类型的不同，对同一种吸附物的吸附机制有时也不同。最后，C10和C14的恢复时间在8.7 fs ~ 0.024 ms之间，光谱的显著变化也支持了C10和C14作为传感器吸附和检测这6种爆炸性或有害化合物的高潜力。方法：采用Gaussian 09软件在M06-2X/6-311G（d,p）、M06-2X- d3 /6-311G（d,p）和M06-2X- d3 /6-311++G（d,p）水平上对结构进行计算。此外，利用Multiwfn软件对其性质和相互作用进行了进一步的计算。

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引用次数: 0

Exploration of a 7.O4O.7 dimeric liquid crystal using temperature-dependent Raman spectroscopy and comparison with density functional theory 探索一个7.40。用温度相关拉曼光谱研究二聚体液晶并与密度泛函理论比较。

IF 2.5 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Modeling

Pub Date : 2025-10-23 DOI: 10.1007/s00894-025-06531-4

Manoj Vishwakarma, Ranjeet Vishwakarma, Kritika Garg, Ayon Bhattacharjee, Debanjan Bhattacharjee

Context

This article focuses on the temperature-dependent Raman spectroscopy analysis of a 7.O4O.7 dimeric liquid crystal, a single molecule. This dimeric compound consists of two symmetric monomers linked by a spacer. This compound exhibits two liquid crystalline phases: SmF and SmA. The article includes the shifting of peak position, variations in integral intensity, and changes in full width at half maximum (FWHM) with temperature fluctuations. The variations in Raman spectral characteristics with temperature provide evidence of charge displacement during phase transitions of the liquid crystal. The orientational and vibrational freedoms of molecules related to Raman bands in relation to temperature variation are also examined. Density functional theoretical approaches were employed to optimise the compound and to compare the Raman spectra at room temperature with experimental Raman data. The experimental and theoretical Raman results align exactly at room temperature, indicating that the basis set and functional employed in this investigation were valid for the 7.O4O.7 dimeric liquid crystal molecule analysed. The assignment of vibrational modes, observed in both experimental and DFT-generated data, was based on potential energy distribution (PED) utilising vibrational energy distribution analysis (VEDA) calculations.

Methods

All theoretical calculations conducted for the study utilised the Gaussian 09 software package. Gauss View 06 and VEDA 4 were employed for the analysis and visualisation of the compounds. The compound had been tuned for optimal performance using the B3LYP functional with the 6-31G (d,p) basis set. Experimental Raman spectroscopy was conducted using the Horiba Lab RAM HR Evolution Raman Spectrometer to obtain temperature-dependent Raman spectra.

背景：本文主要研究了一种7.40 o的温度相关拉曼光谱分析。7二聚体液晶，单分子。这种二聚体化合物由两个对称的单体组成，单体之间由间隔层连接。该化合物具有两种液晶相：SmF和SmA。本文包括峰位置的变化、积分强度的变化以及半峰全宽随温度波动的变化。拉曼光谱特性随温度的变化为液晶相变过程中的电荷位移提供了证据。与拉曼带有关的分子的取向和振动自由与温度变化的关系也进行了研究。采用密度泛函理论方法对化合物进行了优化，并将室温下的拉曼光谱与实验拉曼数据进行了比较。实验和理论拉曼结果在室温下完全一致，表明本研究中使用的基集和函数对7.40 o是有效的。分析了7个二聚体液晶分子。在实验和dft生成的数据中观察到的振动模式的分配是基于利用振动能量分布分析（VEDA）计算的势能分布（PED）。方法：本研究所有理论计算均采用Gaussian 09软件包进行。采用Gauss View 06和VEDA 4对化合物进行分析和可视化。使用6-31G （d,p）基集的B3LYP函数对该化合物进行了优化，以获得最佳性能。利用堀场实验室RAM HR演化拉曼光谱仪进行了实验拉曼光谱分析，获得了温度相关的拉曼光谱。

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