geometrical structure

几何结构
  • 文章类型: Journal Article
    几何结构,相对稳定性,铌碳团簇的电子和磁性,Nb7Cn(n=1-7),在这项研究中进行了调查。密度泛函理论(DFT)计算,再加上桑德斯踢全球搜索,进行了研究Nb7Cn(n=1-7)的结构性质。关于平均结合能的结果,二阶差分能量,离解能,HOMO-LUMO间隙,和化学硬度突出了Nb7C3的强大稳定性。态密度的分析表明,Nb7Cn的分子轨道主要由过渡金属Nb的轨道组成,与最小的C原子的参与。自旋密度和自然种群分析表明,Nb7Cn的总磁矩主要位于Nb原子上。Nb原子对总磁矩的贡献主要来自4d轨道,其次是5p,5s,和6s轨道。
    The geometrical structures, relative stabilities, and electronic and magnetic properties of niobium carbon clusters, Nb7Cn (n = 1-7), are investigated in this study. Density functional theory (DFT) calculations, coupled with the Saunders Kick global search, are conducted to explore the structural properties of Nb7Cn (n = 1-7). The results regarding the average binding energy, second-order difference energy, dissociation energy, HOMO-LUMO gap, and chemical hardness highlight the robust stability of Nb7C3. Analysis of the density of states suggests that the molecular orbitals of Nb7Cn primarily consist of orbitals from the transition metal Nb, with minimal involvement of C atoms. Spin density and natural population analysis reveal that the total magnetic moment of Nb7Cn predominantly resides on the Nb atoms. The contribution of Nb atoms to the total magnetic moment stems mainly from the 4d orbital, followed by the 5p, 5s, and 6s orbitals.
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  • 文章类型: Journal Article
    背景:反式-[Cu(quin)2(EtOH)2],一种新的铜(II)络合物,使用各种计算技术来探索其在药理学应用中的生物学作用。
    方法:计算方法包括密度泛函理论(DFT),ADMET和分子对接。
    结果:优化的几何参数表明,含有Cu离子和喹啉酸盐配体的平面被确认为接近平面。DFT研究结果表明,该配合物具有稳定的结构,具有3.88eV的中等带隙。最高占据分子轨道(HOMO)和最低未占据分子轨道(LUMO)分析显示平面表面分子内电荷转移来自其供体位点,在中心,到它的两端,而不是垂直平面。在分子静电势(MEP)图中观察到氧离子周围的两个富电子区域,这被认为是分子键合和与靶蛋白相互作用的位点。确定药物相似度和药代动力学参数以提供对所研究化合物的安全水平的了解。ADMET(吸收,分布,新陈代谢,排泄,和毒性)结果显示良好的药理特征,口服生物利用度高,毒性风险低。通过将铜络合物拟合到蜡状芽孢杆菌的靶蛋白的活性位点进行分子对接研究,金黄色葡萄球菌,和大肠杆菌。标题复合物在蜡状芽孢杆菌的抑制区内具有最强的抗真菌作用,具有〜9.83kcal/mol的强结合亲和力。此外,与最近报道的其他Cu配合物相比,对金黄色葡萄球菌的活性最大(-6.65kcal/mol)在筛选的参考范围内。对接研究涉及对大肠杆菌细菌的适度抑制活性。
    结论:研究结果强调了该化合物的生物学活性,并将其确定为细菌蜡样芽孢杆菌和金黄色葡萄球菌的可能治疗药物。
    Trans-[Cu (quin)2(EtOH)2], a new copper (II) complex, was characterized using a variety of computational techniques to explore its biological role in pharmacological applications.
    The computational methods included density functional theory (DFT), ADMET and molecular docking.
    The optimized geometrical parameters revealed that the plane containing the Cu ion and the Quinaldinate ligands was confirmed to be nearly planar. DFT findings suggest that the complex has a stable structure with a moderate band gap of 3.88 eV. Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) analysis revealed a planar surface intramolecular charge transfer from its donor sites, in the center, to its ends instead of the vertical plane. Two electron-rich regions were observed around the oxygen ions in the molecular electrostatic potential (MEP) map, which were expected to be the sites of molecular bonding and interactions with target proteins. Drug-likeness and pharmacokinetics parameters were determined to provide insight into the safety level of the studied compound. The ADMET (absorption, distribution, metabolism, excretion, and toxicity) results showed favorable pharmacological features, as evidenced by a high oral bioavailability and a low risk of toxicity. A molecular docking study was performed by fitting the copper complex into the active sites of target proteins for Bacillus cereus, Staphylococcus aureus, and Escherichia coli bacteria. The title complex had the strongest antifungal effect within the inhibitory zone of B. cereus with a strong binding affinity of -9.83 kcal/mol. Also, maximum activity was exhibited against S.aureus (-6.65 kcal/mol) compared to the other recently reported Cu complexes within the limits of the screened references. Docking studies implicated modest inhibitory activity against E. coli bacteria.
    The findings highlighted the compound\'s biological activities and identified it as a possible treatment drug for the bacteria B. cereus and S. aureus.
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  • 文章类型: Journal Article
    在沸腾的乙二醇中将二-(2,6-二氟苯基)马来茚腈与乙酸镁(II)和乙酸锌(II)环化,以合成八-(2,6-二氟苯基)四氮卟啉的Mg(II)和Zn(II)配合物。这些化合物通过UV-Vis鉴定,1HNMR,和质谱法。对八芳基四氮杂卟啉酸镁和锌的光谱发光特性及其对大环苯基片段中氟原子数量和位置的依赖性进行了比较分析。DFT方法用于优化合成复合物的几何结构。应用机器学习方法和QSPR来预测所述络合物的UV-V光谱中的Soret波段波长。
    The cyclization of di-(2,6-difluorophenyl)maleindinitrile with magnesium(II) and zinc(II) acetates in boiling ethylene glycol is applied to synthesize Mg(II) and Zn(II) complexes of the octa-(2,6-difluorophenyl)tetraazaporphyrin. The compounds are identified by UV-Vis, 1H NMR, and mass spectrometry methods. A comparative analysis is performed of the spectral-luminescent properties of magnesium and zinc octaaryltetraazaporphyrinates and their dependence on the number and position of the fluorine atoms in the macrocycle phenyl fragments. The DFT method is used to optimize the geometry of the synthesized complexes. Machine learning methods and QSPR are applied to predict the Soret band wavelength in the UV-V is spectra of the complexes described.
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  • 文章类型: Journal Article
    在这项研究中,具有双-甲亚胺中心键(-CH=N-N=CH-)的一系列新型液晶化合物,即((1E,1\'E)-肼-1,2-二亚烷基双(亚甲基))双(4,1-亚苯基)二烷酸酯(In),是合成的,并对中间相和热性质进行了理论和实验研究。使用元素分析确定了所制备化合物的分子结构,NMR,和FT-IR光谱。通过差示扫描量热法(DSC)检测中间相转变,并使用偏振光学显微镜(POM)鉴定中间相。结果表明,具有最短长度(I5)的衍生物是纯粹的线虫,而其他同系物(I9和I15)具有SmC中间相。从理论上推导了所研究组的最佳几何结构。估计结果表明,所有同系物都是介晶的,它们的类型取决于末端链的长度。基于密度泛函理论(DFT)的计算用于解释实验数据。计算的偶极矩,极化率,热能,和分子静电势都表明可以预测中间相的类型和稳定性,根据分子的大小而变化。
    In this study, a homologous series of novel liquid crystalline compounds bearing the bis-azomethine central linkage (-CH=N-N=CH-), namely ((1E,1\'E)-hydrazine-1,2-diylidenebis(methanylylidene))bis(4,1-phenylene) dialkanoate (In), was synthesized, and the mesophase and thermal properties were investigated theoretically and experimentally. The molecular structures of the prepared compounds were determined using elemental analysis, NMR, and FT-IR spectroscopy. The mesophase transitions were detected by differential scanning calorimetry (DSC), and the mesophases were identified using polarized optical microscopy (POM). The results indicated that the derivative with the shortest length (I5) was purely nematogenic, while the other homologues (I9 and I15) possessed SmC mesophases. The optimal geometrical structures of the investigated group were derived theoretically. The estimated results demonstrated that all homologues were mesomorphic, and their type depended on the length of the terminal chains. Computations based on density functional theory (DFT) were used to explain the experimental data. The calculated dipole moment, polarizability, thermal energy, and molecular electrostatic potential all showed that it was possible to predict the mesophase type and stability, which varied according to the size of the molecule.
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  • 文章类型: Journal Article
    在这里,氟化液晶化合物的新同系物系列,In,合成了4-(((4-氟苯基)亚氨基)甲基)-2-甲氧基苯基4-烷氧基苯甲酸酯,并在实验和理论上研究了其介晶性质。用元素分析仪对合成的化合物进行了表征,NMR,和FT-IR光谱来推断分子结构。差示扫描量热法用于检查中间相转变,而偏振光学显微镜用于鉴定中间相。获得的结果表明,在所有末端侧链中都观察到了纯向列相。除衍生物I8表现出对映性质外,所有同系物均显示具有单向向列介相。从理论上推导了当前设计组的优化几何结构。使用密度泛函理论计算解释了实验数据。偶极矩的估计值,极化率,热能,和分子静电势表明可以说明中间相的稳定性和类型。根据介晶温度范围构建并解决了二元相图,并获得了多晶相。发现末端F原子和侧向CH3O基团的掺入会影响纯状态和混合状态下的构象和空间效应。记录了制备的薄膜的吸收和荧光发射光谱,以阐明末端侧链对合成液晶的光物理性质的影响。人们注意到末端侧链长度的增加导致光学带隙的减小,而电荷载流子寿命增加。
    Herein, a new homologues series of fluorinated liquid crystal compounds, In, 4-(((4-fluorophenyl)imino)methyl)-2-methoxyphenyl 4-alkoxybenzoate were synthesized and its mesomorphic properties were investigated both experimentally and theoretically. The synthesized compounds were characterized by elemental analyzer, NMR, and FT-IR spectroscopy to deduce the molecular structures. The differential scanning calorimetry was employed to examine mesophase transitions whereas the polarized optical microscopy was used to identify the mesophases. The obtained results revealed that the purely nematic phase observed in all terminal side chains. All homologues showed to possess monotropic nematic mesophases except the derivative I8 exhibits enantiotropic property. The optimized geometrical structures of the present designed groups have been derived theoretically. The experimental data was explained using density functional theory computations. The estimated values of dipole moment, polarizability, thermal energy, and molecule electrostatic potential demonstrated that the mesophase stability and type could be illustrated. Binary phase diagram was constructed and addressed in terms of the mesomorphic temperature range and obtained polymorphic phases. It was found that incorporation of the terminal F-atom and lateral CH3O group influence both conformation and steric effect in pure and mixed states. The absorption and fluorescence emission spectra of fabricated films were recorded to elucidate the impact of terminal side chain on photophysical properties of synthesized liquid crystal. It was noted that the increase of terminal side chain length lead to reduction of optical band gap, whereas charge carrier lifetime increases.
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  • 文章类型: Journal Article
    合成了基于三个带有不同长度的末端烷氧基链的芳环的同系物系列,名为4-(4-(烷氧基)苯基亚氨基)甲基)苯基烟酸酯(An)。烷氧基链长度在6、8和16个碳之间变化。通过差示扫描量热法(DSC)和偏振光学显微镜(POM)进行介晶和光学性质。元素分析,进行FT-IR和NMR光谱以阐明所制备衍生物的分子结构。介晶结果表明,所有合成的同系物(An)都是单晶,对映具有向列(N)相,具有广泛的热稳定性。通过密度泛函理论(DFT)理论计算工具测量计算模拟。估计的热和几何参数与实验数据一致。通过讨论估计的参数,发现分子结构,所研究化合物的偶极矩和极化率受到连接的末端柔性链的长度和氮原子在另一个末端芳环中的位置的高度影响。构建了具有不同比例终端的两个相应同源物的二元相图,并从N相的温度范围和稳定性方面讨论了它们的二元相物理性质。
    Homolog series based on three aromatic rings bearing terminal alkoxy chain of various lengths named 4-(4-(alkoxy)phenylimino)methyl)phenyl nicotinate (An) were synthesized. The alkoxy-chain length changed between 6, 8 and 16 carbons. Mesomorphic and optical properties were carried out via differential scanning calorimetry (DSC) and polarized optical microscopy (POM). Elemental analyses, FT-IR and NMR spectroscopy were carried out to elucidate the molecular structures of the prepared derivatives. Mesomorphic results indicated that all the synthesized homologs (An) are monomorphic possessing the nematic (N) phase enantiotropically with wide thermal stability. Computational simulations were measured via density functional theory (DFT) theoretical calculation tool. The estimated thermal and geometrical parameters are in agreement with the experimental data. By discussing the estimated parameters, it was found that the molecular architecture, dipole moment and the polarizability of the investigated compounds are highly affected by the length of the attached terminal flexible chain and the location of the nitrogen atom in the other terminal aromatic ring. Binary phase diagrams of two corresponding homologs with different proportionating terminals were constructed, and their binary phase physical properties were discussed in terms of the temperature range and stability of the N phase.
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  • 文章类型: Journal Article
    两个新的同源物系列,基于带有各种链长的末端烷氧基的偶氮甲碱中心基团的两个环,准备好了。烷氧基链长度在6和16个碳之间变化。第一系列的另一个末端翼是F原子,该化合物命名为N-4-氟苄基-4-(烷氧基)苯胺(In)。第二组化合物除末端F原子外还包括侧位NO2取代基,命名为N-(4-氟-3-硝基亚苄基)-4-(烷氧基)苯胺(IIn)。通过差示扫描量热法(DSC)和偏振光学显微镜(POM)进行介晶和光学性质。元素分析,FT-IR,和NMR光谱进行阐明合成基团的分子结构。中构研究表明,所有合成的同系物(In)都是单态的,具有单调的近晶A(SmA)相位,而第二组(IIn)成员是非介晶的。实验数据表明,中间相的形成受到横向硝基突出的影响。第二组中间相的破坏归因于其分子宽度的增加,影响其横向分子间相互作用。计算模拟与实验数据一致。另一方面,NO2基团在分子几何结构中的位置增加了分子的熔化温度,因此,影响了它们的热和物理性质。通过讨论估计的参数,发现分子结构,偶极矩,所研究化合物的极化率受到末端和侧向取代基的电子性质和位置以及它们的体积的高度影响。
    Two new homologues series, based on two rings of the azomethine central group bearing the terminal alkoxy group of various chain lengths, were prepared. The alkoxy chain length varied between 6 and 16 carbons. The other terminal wing in the first series was the F atom, and the compound is named N-4-florobenzylidene-4-(alkoxy)benzenamine (In). The second group of compounds included a lateral NO2 substituent in addition to the terminal F atom, named N-(4-fluoro-3-nitrobenzylidene)-4-(alkyloxy)aniline (IIn). Mesomorphic and optical properties were carried out via differential scanning calorimetry (DSC) and polarized optical microscopy (POM). Elemental analyses, FT-IR, and NMR spectroscopy were carried out to elucidate the molecular structures of the synthesized groups. Mesomorphic investigations indicated that all the synthesized homologues (In) were monomorphic, possessing the smectic A (SmA) phase monotropically, while the second group (IIn) members were non-mesomorphic. The experimental data indicated that the formation of the mesophase is affected by the protrusion of the lateral nitro group. The disruption of the mesophase in the second group was attributed to the increase of its molecular width, which affects its lateral intermolecular interactions. The computational simulations were in agreement with the experimental data. On the other hand, the location of NO2 group within the molecular geometry increased the melting temperature of the molecule, and thus, affected their thermal and physical properties. By discussing the estimated parameters, it was found that the molecular architecture, the dipole moment, and the polarizability of the investigated compounds are highly affected by the electronic nature and position of the terminal and lateral substituents as well as their volumes.
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  • 文章类型: Journal Article
    最近,牙髓作为多能间充质干细胞(MSCs)的有希望的来源,在再生领域的各种临床应用中受到关注。迄今为止,我们已经成功地建立了在体外条件下显示成牙本质细胞特征的大鼠牙髓来源的细胞。我们把它们命名为牙齿矩阵形成,GFP大鼠来源的细胞(TGC)。然而,尽管TGC在体内条件下形成大量牙本质样的硬组织,这不会导致极性成牙本质细胞的诱导。关注人造生物材料的几何结构对诱导细胞分化和硬组织形成的重要性,我们以前成功地开发了一种新的生物材料,蜂窝状磷酸三钙(TCP)支架,具有各种直径的通孔。在这项研究中,诱导极性成牙本质细胞,使用具有各种孔直径(75、300和500μm)的蜂窝状TCP作为支架,诱导TGC形成成牙本质细胞。结果表明,孔径为300μm的蜂窝状TCP(300TCP)将TGC区分为DSP阳性的极性成牙本质细胞。因此,我们的研究表明,300TCP是一种合适的用于牙本质再生的人工生物材料。
    Recently, dental pulp has been attracting attention as a promising source of multipotent mesenchymal stem cells (MSCs) for various clinical applications of regeneration fields. To date, we have succeeded in establishing rat dental pulp-derived cells showing the characteristics of odontoblasts under in vitro conditions. We named them Tooth matrix-forming, GFP rat-derived Cells (TGC). However, though TGC form massive dentin-like hard tissues under in vivo conditions, this does not lead to the induction of polar odontoblasts. Focusing on the importance of the geometrical structure of an artificial biomaterial to induce cell differentiation and hard tissue formation, we previously have succeeded in developing a new biomaterial, honeycomb tricalcium phosphate (TCP) scaffold with through-holes of various diameters. In this study, to induce polar odontoblasts, TGC were induced to form odontoblasts using honeycomb TCP that had various hole diameters (75, 300, and 500 μm) as a scaffold. The results showed that honeycomb TCP with 300-μm hole diameters (300TCP) differentiated TGC into polar odontoblasts that were DSP positive. Therefore, our study indicates that 300TCP is an appropriate artificial biomaterial for dentin regeneration.
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  • 文章类型: Journal Article
    人工生物材料的几何结构对颅骨再生的影响尚不清楚。在之前的研究中,我们成功开发了蜂窝状β-磷酸三钙(β-TCP),具有贯通孔,能够为骨组织再生提供最佳的骨微环境。我们证明了孔直径为300μm的β-TCP诱导了剧烈的骨形成。在本研究中,我们研究了蜂窝状β-TCP(水平或垂直孔)的孔方向差异如何影响颅骨缺损中的骨组织再生。以基质胶和胶原蛋白凝胶为载体,用BMP-2负载具有垂直和水平孔的蜂窝β-TCP,并移植到大鼠颅骨骨缺损模型中。结果表明,在每四组(单独胶原蛋白组,单独使用Matrigel组,胶原蛋白+BMP组和Matrigel+BMP-2),与水平β-TCP相比,在垂直β-TCP上观察到剧烈的骨形成。在垂直β-TCP和水平β-TCP中,基质胶组(有和没有BMP-2)的成骨面积均大于胶原蛋白组(有和没有BMP-2)。然而,当添加BMP-2时,在垂直β-TCP中,胶原蛋白组和Matrigel组之间的骨形成面积没有显着差异。组织学发现表明,在垂直蜂窝β-TCP中,新骨形成延伸到孔的上部,并从硬脑膜侧到骨膜侧观察到,添加到孔的内壁。因此,我们可以通过创建由垂直蜂窝状β-TCP提供的骨骼微环境来控制有效的骨骼形成。垂直蜂窝状β-TCP有潜力成为颅骨缺损中骨组织再生的优异生物材料,并有望在临床上应用。
    The effect of the geometric structure of artificial biomaterials on skull regeneration remains unclear. In a previous study, we succeeded in developing honeycomb β-tricalcium phosphate (β-TCP), which has through-and-through holes and is able to provide the optimum bone microenvironment for bone tissue regeneration. We demonstrated that β-TCP with 300-μm hole diameters induced vigorous bone formation. In the present study, we investigated how differences in hole directions of honeycomb β-TCP (horizontal or vertical holes) influence bone tissue regeneration in skull defects. Honeycomb β-TCP with vertical and horizontal holes was loaded with BMP-2 using Matrigel and Collagen gel as carriers, and transplanted into skull bone defect model rats. The results showed that in each four groups (Collagen alone group, Matrigel alone group, Collagen + BMP group and Matrigel + BMP-2), vigorous bone formation was observed on the vertical β-TCP compared with horizontal β-TCP. The osteogenic area was larger in the Matrigel groups (with and without BMP-2) than in the Collagen group (with and without BMP-2) in both vertical β-TCP and horizontal β-TCP. However, when BMP-2 was added, the bone formation area was not significantly different between the Collagen group and the Matrigel group in the vertical β-TCP. Histological finding showed that, in vertical honeycomb β-TCP, new bone formation extended to the upper part of the holes and was observed from the dura side to the periosteum side as added to the inner walls of the holes. Therefore, we can control efficient bone formation by creating a bone microenvironment provided by vertical honeycomb β-TCP. Vertical honeycomb β-TCP has the potential to be an excellent biomaterial for bone tissue regeneration in skull defects and is expected to have clinical applications.
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  • 文章类型: Journal Article
    Single-atom catalysts have become a hot spot because of the high atom utilization efficiency and excellent activity. However, the effect of the support structure in the single-atom catalyst is often unnoticed in the catalytic process. Herein, a series of carbon spheres supported Ni-N4 single-atom catalysts with different support structures are successfully synthesized by the fine adjustment of synthetic conditions. The hollow mesoporous carbon spheres supported Ni-N4 catalyst (Ni/HMCS-3-800) exhibits superior catalytic activity toward the electrocatalytic CO2 reduction reaction (CO2 RR). The Faradaic efficiency toward CO is high to 95% at the potential range from -0.7 to -1.1 V versus reversible hydrogen electrode and the turnover frequency value is high up to 15 608 h-1 . More importantly, the effect of the geometrical structures of carbon support on the CO2 RR performance is studied intensively. The shell thickness and compactness of carbon spheres regulate the chemical environment of the doped-N species in the carbon skeleton effectively and promote CO2 molecule activation. Additionally, the optimized mesopore size is beneficial to improve diffusion and overflow of the substance, which enhances the CO2 adsorption capacity greatly. This work provides a new consideration for promoting the catalytic performance of single-atom catalysts.
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