DFT calculations

DFT 计算
  • 文章类型: Journal Article
    在此,我们已经证明了有利的π-孔Br···金属非共价相互作用(NCI)的形成,涉及第9、11和12族元素。更详细地说,M(M=Co2+,Ni2+,已合成了含Cu2和Zn2)的卟啉,并通过单晶X射线衍射和Hirshfeld表面分析对其结构进行了表征,除了辅助氢键和孤对键外,还揭示了定向Br··M接触的形成。在PBE0-D3/def2-TZVP理论水平上的计算揭示了Br···M相互作用的π孔性质。此外,使用量子化学方法研究了这些NCI的物理性质,提供了Zn2+和Cu2+卟啉中π-孔Spedium和Regium键的证据,除了揭示第9组(Co2)的π孔的存在。另一方面,第10组(Ni2)同时充当电子供体和受体部分,而不显示正电子π-空穴。由于过渡金属化学中π-空穴相互作用的潜力不足,我们相信本文报道的结果将在超分子化学中有用,有机金属化合物,和固态化学,即i)将涉及第一行过渡金属的π孔化学置于聚光灯下,以及ii)解锁一种新工具以指导金属卟啉的自组装。
    Herein we have evidenced the formation of favorable π-hole Br···metal noncovalent interactions (NCIs) involving elements from groups 9, 11 and 12. More in detail, M (M = Co2+, Ni2+, Cu2+ and Zn2+) containing porphyrins have been synthesized and their supramolecular assemblies structurally characterized by means of single crystal X-ray diffraction and Hirshfeld surface analyses, revealing the formation of directional Br···M contacts in addition to ancillary hydrogen bond and lone pair-π bonds. Computations at the PBE0-D3/def2-TZVP level of theory revealed the π-hole nature of the Br···M interaction. In addition, the physical nature of these NCIs was studied using Quantum Chemistry methodologies, providing evidence of π-hole Spodium and Regium bonds in Zn2+ and Cu2+ porphyrins, in addition to unveiling the presence of  a π-hole for group 9 (Co2+). On the other hand, group 10 (Ni2+) acted as both electron donor and acceptor moiety without showing an electropositive π-hole. Owing to the underexplored potential of π-hole interactions in transition metal chemistry, we believe the results reported herein will be useful in supramolecular chemistry, organometallics, and solid-state chemistry by i) putting under the spotlight the π-hole chemistry involving first row transition metals and ii) unlocking a new tool to direct the self-assembly of metalloporphyrins.
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  • 文章类型: Journal Article
    在同形mer-[IrX3(THT)(CNXyl)2](X=Cl1,Br2;THT=四氢噻吩;Xyl=2,6-Me2C6H3-)络合物的X射线结构中,我们揭示了异氰化物甲基的C原子与另一个分子的卤化物配体之间的短分子间接触。对X射线数据的几何考虑和对适当的DFT研究的分析允许将这些接触归因于CMe···X-IrIII(X=Cl,Br)tetrel键。具体来说,通过DFT计算和各种理论模型的应用,Tetrel键合相互作用的存在得到了验证,并评估了CMe···X-IrIII相互作用的贡献。通过分子静电势(MEP)表面计算,证明了在异氰化物配位到铱(III)时tetrel键的增强。为了区分CMe···X-IrIII(X=Cl,Br)来自常规氢键的相互作用,我们采用了多种计算方法,包括自然键轨道(NBO)分析和电子定位函数(ELF)分析。此外,将能量分解分析(EDA)应用于选定的模型系统,以探索这些相互作用的潜在物理性质。
    In X-ray structures of the isomorphic mer-[IrX3(THT)(CNXyl)2] (X = Cl 1, Br 2; THT = tetrahydrothiophene; Xyl = 2,6-Me2C6H3-) complexes, we revealed short intermolecular contacts between the C-atom of an isocyanide methyl group and halide ligands of another molecule. Geometrical consideration of the X-ray data and analysis of appropriate DFT studies allowed the attribution of these contacts to CMe···X-IrIII (X = Cl, Br) tetrel bond. Specifically, through the application of DFT calculations and various theoretical models, the presence of tetrel bonding interactions was validated, and the contribution of the CMe···X-IrIII interaction was assessed. The reinforcement of the tetrel bond upon the isocyanide coordination to iridium(III) is substantiated by molecular electrostatic potential (MEP) surface calculations. To distinguish the tetrel bonding characteristics of CMe···X-IrIII (X = Cl, Br) interactions from conventional hydrogen bonding, we employed multiple computational methodologies, including Natural Bond Orbital (NBO) analysis and Electron Localization Function (ELF) analysis. Additionally, Energy Decomposition Analysis (EDA) was applied to selected model systems to explore the underlying physical nature of these interactions.
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  • 文章类型: Journal Article
    (1)背景:制药的使用越来越多,需要长期发展有效的策略,包括定制高度特定的新材料以将其从环境中移除。光催化降解一直是该领域研究人员日益关注的主题。(2)方法:本文主要研究了在TiO2表面沉积一层薄金属层的可能性,并采用理论和实验相结合的方法研究了其光催化降解环丙沙星的性能。(3)结果:基于24d金属在TiO2上的附着力的广泛DFT筛选,选择Cu进行进一步的工作,由于令人满意的预期稳定性和良好的可用性。成功合成了(Cu)TiO2,并用XRD对其进行了表征,SEM+EDS和UV-Vis分光光度法。TiO2表面上均匀分布的铜对应于在高亲和力富氧位点上的结合,如DFT计算所提出的。与裸露的未改性TiO2相比,环丙沙星的光催化降解速率提高了约1.5倍。(4)结论:观察到的结果归因于吸附的Cu能够阻止TiO2的团聚并增加活性催化面积,以及通过DFT计算预测的带隙变窄。
    (1) Background: An increasing use of pharmaceutics imposes a need for the permanent development of efficient strategies, including the tailoring of highly specific new materials for their removal from the environment. Photocatalytic degradation has been the subject of increasing interest of the researchers in the field. (2) Methods: This paper is focused on the investigation of the possibility to deposit a thin metal layer on a TiO2 surface and study its photocatalytic performance for the degradation of ciprofloxacin using a combination of theoretical and experimental methods. (3) Results: Based on the extensive DFT screening of 24 d-metals\' adhesion on TiO2, Cu was selected for further work, due to the satisfactory expected stability and good availability. The (Cu)TiO2 was successfully synthesized and characterized with XRD, SEM+EDS and UV-Vis spectrophotometry. The uniformly distributed copper on the TiO2 surface corresponds to the binding on high-affinity oxygen-rich sites, as proposed with DFT calculations. The photocatalytic degradation rate of ciprofloxacin was improved by about a factor of 1.5 compared to the bare non-modified TiO2. (4) Conclusions: The observed result was ascribed to the ability of adsorbed Cu to impede the agglomeration of TiO2 and increase the active catalytic area, and bandgap narrowing predicted with DFT calculations.
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  • 文章类型: Journal Article
    我们建立了一个计算机模拟实验,并设计了一种嵌合化合物,该化合物整合了来自不同高效ROS(活性氧)清除剂的分子特征,目的是研究分子结构与抗氧化活性之间的潜在关系。此外,由于已知的减少氢过氧化物的能力,插入了一个硒中心,充当谷胱甘肽过氧化物酶的分子模拟物;最后,由于这种有机硒化物是N-杂环卡宾配体的前体,设计并检查了其Au(I)卡宾络合物。采用基于DFT(密度泛函理论)的经过验证的方案来研究有机硒化物前体((SMD)-M06-2X/6-311G(d,p)//M06-2X/6-31G(d)),以及有机金属配合物((SMD)-M06-2X/SDD(Au),6-311+G(d,p)//ZORA-BLYP-D3(BJ)/TZ2P),考虑HAT(氢原子转移)和RAF(自由基加合物形成)关于五个不同的自由基。本案例研究的结果表明,在设计嵌合化合物时,化学基序的抗氧化潜力不应被视为添加剂。而是分子拓扑结构的相关性来自与分子的适当化学空间相结合的化学基序。因此,通常被认为是抗氧化剂本身的单一官能团的直接贡献并不能保证分子物种的有效自由基清除潜力。
    We set up an in silico experiment and designed a chimeric compound integrating molecular features from different efficient ROS (Reactive Oxygen Species) scavengers, with the purpose of investigating potential relationships between molecular structure and antioxidant activity. Furthermore, a selenium centre was inserted due to its known capacity to reduce hydroperoxides, acting as a molecular mimic of glutathione peroxidase; finally, since this organoselenide is a precursor of a N-heterocyclic carbene ligand, its Au(I) carbene complex was designed and examined. A validated protocol based on DFT (Density Functional Theory) was employed to investigate the radical scavenging activity of available sites on the organoselenide precursor ((SMD)-M06-2X/6-311+G(d,p)//M06-2X/6-31G(d)), as well as on the organometallic complex ((SMD)-M06-2X/SDD (Au), 6-311+G(d,p)//ZORA-BLYP-D3(BJ)/TZ2P), considering HAT (Hydrogen Atom Transfer) and RAF (Radical Adduct Formation) regarding five different radicals. The results of this case study suggest that the antioxidant potential of chemical motifs should not be considered as an additive property when designing a chimeric compound, but rather that the relevance of a molecular topology is derived from a chemical motif combined with an opportune chemical space of the molecule. Thus, the direct contributions of single functional groups which are generally thought of as antioxidants per se do not guarantee the efficient radical scavenging potential of a molecular species.
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  • 文章类型: Journal Article
    聚对苯二甲酸乙二醇酯(PET)微塑料和纳米塑料以大气和空气传播形式(PET-aMPs)普遍存在于大气中。使用第一原理计算,我们分析了主要空气污染物在PET-AMPs上的吸收,专注于他们的稳定性,吸附机制,和热化学。结果表明,PET-aMPs对CO的自发吸附具有选择性,CO2,NO,N2O,NO2,NH3和SO2,达到每分子6-20kcal/mol的稳定吸附能,具有与碳基材料相当的吸收能力,金属/准金属,和金属氧化物表面。然后,PET-aMPs成为大气中共存空气污染物的载体,根据气态分子的分子极性(偶极矩)和原子组成(电负性),通过内部或外部吸附进行吸附。此外,大气中的H2O和O2不是竞争性分子,由于表面氧化和结构破坏,臭氧可以增强吸附。静电(46-61%)和分散力(21-58%)的相互作用驱动了吸附机制,低极性污染物几乎显示出平衡的静电与色散贡献,而高极性分子显示出更高的静电稳定性。通过强分散达到外部吸附,氢键,和偶极-偶极感应对,而孤对电子相互作用出现在内部吸附状态中。这些结果扩大了对大气和空气中的微塑料/纳米塑料的危害和风险的理解,他们的影响,共同运输能力,与环境的互动。
    Polyethylene terephthalate (PET) microplastics and nanoplastics are ubiquitously present in the atmosphere as atmospheric and airborne forms (PET-aMPs). Using first-principles calculations, we analyze the uptake of primary air pollutants onto PET-aMPs, focusing on their stabilities, adsorption mechanisms, and thermochemistry. The results show that PET-aMPs are selective for the spontaneous adsorption of CO, CO2, NO, N2O, NO2, NH3, and SO2, reaching stable adsorption energies of 6-20 kcal/mol per molecule, with comparable uptake ability than carbon-based materials, metals/metalloids, and metal oxide surfaces. Then, PET-aMPs become a vector for coexisting air pollutants in the atmosphere, which adsorb by inner or outer adsorption depending on the molecular polarity (dipole moment) and atomic constitution (electronegativity) of gaseous molecules. Also, atmospheric H2O and O2 are not competitive molecules, and ozone could enhance adsorption due to surface oxidation and structure breakdown. The interplay of electrostatic (46-61%) and dispersion forces (21-58%) drives the adsorption mechanism, where low-polar pollutants display almost a balanced electrostatic vs. dispersion contribution, while high polar molecules display a higher electrostatic stabilization. The outer adsorption is reached by strong dispersion, hydrogen bonding, and dipole-dipole-induced pairs, while lone-pair-π interactions appear in the inner adsorption regime. These results expand the understanding of the hazards and risks of atmospheric and airborne microplastics/nanoplastics, their impacts, co-transport ability, and interaction with the environment.
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  • 文章类型: Journal Article
    研磨后发现3-[1-(叔丁氧基羰基)氮杂环丁烷-3-基]-1,2-恶唑-4-甲酸的多晶型转变。对晶体结构转变之前和之后的多晶型结构的深入研究揭示了多晶型转变的一些先决条件以及分子和晶体结构变化的规律。在亚稳态多晶型物1a中,构象柔性分子采用具有较高能量的构象,并形成不太优选的线性超分子合成子。在研磨过程中赋予晶体结构的额外能量被证明足以克服氮反转和恶唑环围绕sp3-sp2单键旋转的低能垒。因此,获得了多晶型物1b,其分子采用具有较低能量的构象并形成更优选的中心对称超分子合成子。对两种多晶型物的成对相互作用能的研究表明,亚稳态多晶型物1a由分子构建单元组织,具有柱状层状结构。中心对称二聚体应被认为是更稳定的多晶型物1b中的复杂结构单元,具有分层结构。
    A polymorphic transition as a result of grinding was found for 3-[1-(tert-butoxycarbonyl)azetidin-3-yl]-1,2-oxazole-4-carboxylic acid. The thorough study of polymorphic structures before and after crystal structure transformation has revealed some pre-conditions for a polymorphic transition and regularities of changes in molecular and crystal structure. In metastable polymorph 1a, the conformationally flexible molecule adopts a conformation with the higher energy and forms a less preferable linear supramolecular synthon. Additional energy imparted to a crystal structure during the grinding process proved to be enough to overcome low energy barriers for the nitrogen inversion and rotation of the oxazole ring around the sp3-sp2 single bond. As a result, polymorph 1b with a molecule adopting conformation with lower energy and forming a more preferable centrosymmetric supramolecular synthon was obtained. The study of pairwise interaction energies in the two polymorphs has shown that metastable polymorph 1a is organized by molecular building units and has a columnar-layered structure. A centrosymmetric dimer should be recognized as a complex building unit in more stable polymorph 1b, which has a layered structure.
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  • 文章类型: Journal Article
    The existence of areas of strongly positive electrostatic potential in the central regions of the molecular surface of high-energy molecules is a strong indicator that these compounds are very sensitive towards detonation. Development of high-energy compounds with reduced sensitivity towards detonation and high efficiency is hard to achieve since the energetic molecules with high performance are usually very sensitive. Here we used Density Functional Theory (DFT) calculations to study a series of bis(acetylacetonato) and nitro-bis(acetylacetonato) complexes and to elucidate their potential application as energy compounds with moderate sensitivities. We calculated electrostatic potential maps for these molecules and analyzed values of positive potential in the central portions of molecular surfaces in the context of their sensitivity towards detonation. Results of the analysis of the electrostatic potential demonstrated that nitro-bis(acetylacetonato) complexes of Cu and Zn have similar values of electrostatic potential in the central regions (25.25 and 25.06 kcal/mol, respectively) as conventional explosives like TNT (23.76 kcal/mol). Results of analysis of electrostatic potentials and bond dissociation energies for the C-NO2 bond indicate that nitro-bis(acetylacetonato) complexes could be used as potential energetic compounds with satisfactory sensitivity and performance.
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  • 文章类型: Journal Article
    作为在金(I)催化的级联反应中形成顺式或反式稠合双环[5.1.0]辛烷的机理研究的一部分,已经重新检查了环丙基金(I)卡宾型中间体的性质。DFT方法的基准以及QTAIM理论和NBO分析证实了在烯炔的环异构化中形成具有卡宾或碳阳离子结构的不同中间体。
    The nature of cyclopropyl gold(I) carbene-type intermediates has been reexamined as part of a mechanistic study on the formation of cis- or trans-fused bicyclo[5.1.0]octanes in a gold(I)-catalyzed cascade reaction. Benchmark of DFT methods together with QTAIM theory and NBO analysis confirms the formation of distinct intermediates with carbenic or carbocationic structures in the cycloisomerizations of enynes.
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  • 文章类型: Journal Article
    High-throughput calculations can be applied to a large number of compounds, in order to discover new useful materials. In the present work, ternary intermetallic compounds are investigated, to find new potentially interesting materials for thermoelectric applications. The screening of stable nonmetallic compounds required for such applications is performed by calculating their electronic structure, using DFT methods. In the first section, the study of the density of states at the Fermi level, of pure elements, binary and ternary compounds, leads to empirically chose the selection criterion to distinguish metals from nonmetals. In the second section, the TiNiSi structure-type is used as a case-study application, through the investigation of 570 possible compositions. The screening leads to the selection of 12 possible semiconductors. The Seebeck coefficient and the lattice thermal conductivity of the selected compounds are calculated in order to identify the most promising ones. Among them, TiNiSi, TaNiP, or HfCoP are shown to be worth a detailed experimental investigation.
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  • 文章类型: Journal Article
    两个三萜(14S,17S,20S,24R)-25-羟基-14,17-环-20,24-环氧-malabarican-3-酮(CEM,1a)和(14S,17S,20S,24R)-20,24,25-三羟基-14,17-环马沙拉巴蛋白聚糖-3-酮(CM,2a)与环丁烷环进行了报道,具有与ocotillone(1b)和gardubryoneC(2b)相同的NMR数据,分别。可能会报告不正确的结构。因此,通过CASE算法和DFT化学位移预测实现了这些三萜的结构再分析,结果表明,CEM和CM的结构可能不正确。为了进一步验证化合物1的结构,HMBC,采用1H-1HCOSY和HSQC-TOCSY光谱。在这里,我们修改了CEM和CM的结构,我们的研究还表明,CASE算法和DFT化学位移预测可以支持有效的结构重新分配方法。
    Two triterpenes (14S,17S,20S,24R)-25-hydroxy-14,17-cyclo-20,24-epoxy-malabarican-3-one (CEM, 1a) and (14S,17S,20S,24R)-20,24,25-trihydroxy-14,17-cyclomalabarican-3-one (CM, 2a) with a cyclobutane ring were reported, which have the same NMR data as ocotillone (1b) and gardaubryone C (2b), respectively. An incorrect structure might be reported. Therefore, the structure reanalysis of these triterpenes was achieved by CASE algorithm and DFT chemical shift predictions, and the results showed that the structures of CEM and CM might be incorrect. To further verify the structure of compound 1, the HMBC, 1H-1H COSY and HSQC-TOCSY spectra were employed. Herein, we revised the structure of CEM and CM, and our study also showed that CASE algorithm and DFT chemical shift predictions can hold the post of effective structure reassignment method.
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