DFT calculations

DFT 计算
  • 文章类型: Journal Article
    应变碳环结构单元的合成与药物化学有关,和亚甲基环丁烷在当前的合成技术中尤其具有挑战性。仔细检查[1.1.1]推进剂和二硼试剂的反应性,发现双(儿茶酚)二硼(B2cat2)可以在室温下在几分钟内产生双(硼化)亚甲基环丁烷。该反应构成了通过特殊的非极性烃活化B-B键的第一个例子,也是第一次用硼亲电活化推进剂。包括原位NMR动力学和DFT计算在内的机理研究表明,二硼部分可以通过与推进剂的倒σ键配位而直接活化。并揭示DMF参与二硼酸酯中间体的稳定而不是B-B键的活化。这些结果为二硼和推进剂化学提供了新的可能性,并进一步发展了基于推进剂菌株释放的亚甲基环丁烷的合成。
    The synthesis of strained carbocyclic building blocks is relevant for Medicinal Chemistry, and methylenecyclobutanes are particularly challenging with current synthetic technology. Careful inspection of the reactivity of [1.1.1]propellane and diboron reagents has revealed that bis(catecholato)diboron (B2cat2) can produce a bis(borylated) methylenecyclobutane in a few minutes at room temperature. This reaction constitutes the first example of B-B bond activation by a special apolar hydrocarbon and also the first time that propellane is electrophilically activated by boron. Mechanistic studies including in situ NMR kinetics and DFT calculations demonstrate that the diboron moiety can be directly activated through coordination with the inverted sigma bond of propellane, and reveal that DMF is involved in the stabilization of diboronate ylide intermediates rather than the activation of the B-B bond. These results enable new possibilities for both diboron and propellane chemistry, and for further developments in the synthesis of methylenecyclobutanes based on propellane strain release.
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  • 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
    文献中以一般方式阐述了由Isatin和肌氨酸形成甲亚胺叶立德的反应机理。这项计算研究旨在详细探索该反应的机理步骤,并评估在1,3-偶极环加成反应中形成的叶立德与7-氧杂苯并苯降冰片二烯的反应性。为此,M06-2X上的密度泛函理论(DFT)计算(SMD,EtOH)/6-31G(d,P)水平被采用。结果表明,消除CO2是速率决定步骤,1,3-偶极环加成的活化屏障较低,并且所形成的叶立德将容易地与双极化体反应。用电子撤回基团取代isatine会稍微降低叶立德形成的激活屏障。
    The reaction mechanism of tthe formation of azomethine ylides from isatins and sarcosine is addressed in the literature in a general manner. This computational study aims to explore the mechanistic steps for this reaction in detail and to assess the reactivity of formed ylide in a 1,3-dipolar cycloaddition reaction with 7-oxabenzonorbornadiene. For this purpose, density functional theory (DFT) calculations at the M06-2X(SMD,EtOH)/6-31G(d,p) level were employed. The results indicate that CO2 elimination is the rate-determining step, the activation barrier for 1,3-dipolar cycloaddition is lower, and the formed ylide will readily react with dipolarophiles. The substitution of isatine with electron-withdrawal groups slightly decreases the activation barrier for ylide formation.
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  • 文章类型: Journal Article
    苄腈(BZN)和四氯化碳(CCl4)是用作合成许多产物的前体的通用溶剂。作为多用途分子,这些化合物可能涉及可持续的化学过程,例如冷等离子体技术,已知产生的电子负责反应。因此,希望探索低能量电子与气相中的共化合物的相互作用。氯和花青阴离子的产生,由与CCl4和BZN的电子碰撞引发,分别,与前体分子进行亲核取代SN2反应,以合成氯苯和三酚乙腈。通过DFT计算合理化了苄腈的断裂机理和合成反应。离子反应产生的花青阴离子的产率随着混合气体的温度而增加,在25°C-100°C的温度范围内探测。本工作可能有助于例如通过(冷)等离子体技术生产氯苯的潜在方法。
    Benzonitrile (BZN) and carbon tetrachloride (CCl4) are versatile solvents used as a precursor for the synthesis of many products. As multi-usage molecules, these compounds may be involved in sustainable chemistry processes such as the cold plasma techniques for which the generated electrons are known to be responsible for reactions. Therefore, it is desirable to explore the interaction of low energy electrons with the co-compounds in the gas phase. The production of chlorine and cyanine anions, initiated by the electron collision with CCl4 and BZN, respectively, undergo nucleophilic substitution SN2 reaction with the precursors molecules for the synthesis of chlorobenzene and tricholoacetonitrile. The mechanism of fragmentation of benzonitrile and the synthesis reactions are rationalized by DFT calculations.  The yield of the cyanine anion produced from the ion reaction increases with the temperature of the admixture gas, probed in the 25 °C-100 °C temperature range. The present work may contribute to a potential process for the production of chlorobenzene for instance via (cold) plasma techniques.
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  • 文章类型: Journal Article
    含呋喃化合物在食品中广泛分布,草药,工业合成产品,环境媒体。这些化合物可以在生物体内经历细胞色素P450酶(CYP450)催化的氧化代谢,这可能会产生反应产物,可能与生物分子反应以引起毒性作用。在这项工作中,我们进行了DFT计算,以2-甲基呋喃作为模型底物,研究CYP450介导的呋喃环氧化的代谢机制,同时,我们研究了涉及2-甲基呋喃甲基的另一个羟基化反应的区域选择性竞争。因此,我们发现毒理学相关的顺式-烯二酮产品可以通过协同方式直接从O-加成产生,而不会像传统上认为的那样形成环氧化物中间体。此外,我们的计算证明了呋喃环氧化和甲基羟基化途径的动力学和热力学可行性,虽然前一种途径更有利。然后,我们构建了一个线性模型,以根据其绝热电离电势(AIP)和冷凝Fukui函数(CFF)预测具有11种不同呋喃子化合物的O加成的限速活化能(ΔE*)。结果显示良好的预测能力(R2=0.94,Q2CV=0.87)。因此,AIP和CFF具有与机制相关的明确物理含义,作为关键分子描述符出现,以便快速预测呋喃环氧化反应性,从而快速了解呋喃的毒理学风险,只使用基态计算。
    Furan-containing compounds distribute widely in food, herbal medicines, industrial synthetic products, and environmental media. These compounds can undergo oxidative metabolism catalyzed by cytochrome P450 enzymes (CYP450) within organisms, which may produce reactive products, possibly reacting with biomolecules to induce toxic effects. In this work, we performed DFT calculations to investigate the CYP450-mediated metabolic mechanism of furan-ring oxidation using 2-methylfuran as a model substrate, meanwhile, we studied the regioselective competition of another hydroxylation reaction involving methyl group of 2-methylfuran. As a result, we found the toxicological-relevant cis-enedione product can be produced from O-addition directly via a concerted manner without formation of an epoxide intermediate as traditionally believed. Moreover, our calculations demonstrate the kinetic and thermodynamic feasibility of both furan-ring oxidation and methyl hydroxylation pathways, although the former pathway is a bit more favorable. We then constructed a linear model to predict the rate-limiting activation energies (ΔE*) of O-addition with 11 diverse furan substates based on their adiabatic ionization potentials (AIPs) and condensation Fukui functions (CFFs). The results show a good predictive ability (R2=0.94, Q2CV=0.87). Therefore, AIP and CFF with clear physichem meanings relevant to the mechanism, emerge as pivotal molecular descriptors to enable the fast prediction of furan-ring oxidation reactivities for quick insight into the toxicological risk of furans, using just ground-state calculations.
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  • 文章类型: Journal Article
    固态光催化的理论模型是重要的问题之一,因为迄今为止已经开发了各种有用的光催化剂。在这项工作中,我们研究了通过实验开发的氧化铌(Nb2O5)上的醇光氧化机理,采用密度泛函理论(DFT)/时间依赖(TD)的基于聚类模型的DFT计算。醇吸附和从羟基到表面的第一次氢转移发生在基态,而在紫外线或可见光的光照射过程中,从CH的第二次氢转移以激发态进行。鉴定了自旋交叉,并解决了反应途径的低处三重态。可见光区的光吸收表征为从醇的O2p到Nb2O5表面的Nb4d的电荷转移转变。自旋密度和自然种群分析表明羰基化合物部分自旋密度的产生及其耗散到表面界面,部分解释了电子顺磁共振测量。与实验速率方程分析一致,证实了速率确定步骤是羰基化合物和水分子的解吸。理论模型的研究结果将为固态光催化的进一步研究提供有用的信息。
    Theoretical modeling of the solid-state photocatalysis is one of the important issues as various useful photocatalysts have been developed to date. In this work, we investigated the mechanism of the alcohol photooxidation on niobium oxide (Nb2O5) which was experimentally developed, using the density functional theory (DFT)/time-dependent (TD)DFT calculations based on the cluster model. The alcohol adsorption and the first hydrogen transfer from hydroxy group to surface occur in the ground state, while the second hydrogen transfer from CH proceeds in the excited states during the photoirradiation of UV or visible light. The spin crossing was identified and the low-lying triplet states were solved for the reaction pathway. The photoabsorption in the visible light region was characterized as the charge transfer transition from O 2p of alcohol to Nb 4d of the Nb2O5 surface. The spin density and the natural population analysis indicated the generation of spin density in the moiety of carbonyl compound and its dissipation to the interface of the surface, which partly explains the electron paramagnetic resonance measurement. It was confirmed that the rate determining step is the desorption of carbonyl compound and water molecule in agreement with the experimental rate equation analysis. The present findings with the theoretical modeling will provide useful information for the further studies of the solid-state photocatalysis.
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  • 文章类型: Journal Article
    在这项研究中,我们研究了长程氟-碳J偶联确定脱氧氟二糖结构的潜力。三种二糖,先前合成为潜在的半乳糖凝集素抑制剂,表现出穿过空间的氟碳J耦合。在我们对这些二糖衍生物的独立构象分析中,我们采用了密度泛函理论(DFT)计算和核磁共振(NMR)实验的组合。通过将计算出的核屏蔽与实验碳化学位移进行比较,我们能够确定每种化合物最可能的构象异构体。使用包含氟甲烷和甲烷分子的模型来研究分子排列与分子间通过空间J偶联之间的关系。我们的研究证明了核间距离和分子取向对氟碳耦合的大小的重要影响。二糖的氟-碳通过空间偶联(TSC)的实验值与通过构象分析鉴定的最可能构象异构体的计算值相对应。这些结果揭示了氟-碳TSC作为柔性分子构象分析的强大工具的更广泛的应用。为未来的结构研究提供有价值的见解。
    In this study, we investigated the potential of long-range fluorine-carbon J-coupling for determining the structures of deoxyfluorinated disaccharides. Three disaccharides, previously synthesized as potential galectin inhibitors, exhibited through-space fluorine-carbon J-couplings. In our independent conformational analysis of these disaccharide derivatives, we employed a combination of density functional theory (DFT) calculations and nuclear magnetic resonance (NMR) experiments. By comparing the calculated nuclear shieldings with the experimental carbon chemical shifts, we were able to identify the most probable conformers for each compound. A model comprising fluoromethane and methane molecules was used to study the relationship between molecular arrangements and intermolecular through-space J-coupling. Our study demonstrates the important effect of internuclear distance and molecular orientation on the magnitude of fluorine-carbon coupling. The experimental values for the fluorine-carbon through-space couplings (TSCs) of the disaccharides corresponded with values calculated for the most probable conformers identified by the conformational analysis. These results unlock the broader application of fluorine-carbon TSCs as powerful tools for conformational analysis of flexible molecules, offering valuable insights for future structural investigations.
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  • 文章类型: Journal Article
    席夫碱(SB)由于其独特的结构性质,在配位化学中是重要的配体。它们与金属离子形成络合物的能力已被用于对新兴的水污染物进行环境检测。在这项工作中,我们评估了三个新提出的SB的络合能力,1-3,通过完整的构象分析,结合分子动力学和密度泛函理论研究,了解它们协调有毒重金属(HM)离子的能力。从这项研究中,它出现了所有的配体呈现的几何形状,使它们适合于通过N-亚氨基部分络合HM,或,在3的情况下,以氧原子为载体的乙烯二醚链。特别是,这种配体显示出最有希望的配位行为,特别是Pb2+。
    Schiff bases (SBs) are important ligands in coordination chemistry due to their unique structural properties. Their ability to form complexes with metal ions has been exploited for the environmental detection of emerging water contaminants. In this work, we evaluated the complexation ability of three newly proposed SBs, 1-3, by complete conformational analysis, using a combination of Molecular Dynamics and Density Functional Theory studies, to understand their ability to coordinate toxic heavy metal (HMs) ions. From this study, it emerges that all the ligands present geometries that make them suitable to complex HMs through the N-imino moieties or, in the case of 3, with the support of the oxygen atoms of the ethylene diether chain. In particular, this ligand shows the most promising coordination behavior, particularly with Pb2+.
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  • 文章类型: Journal Article
    半导体过渡金属二硫属化物(TMD)的自下而上合成路线的开发及其缺陷的评估对于实现其应用至关重要。通过化学气相沉积(CVD)生长的TMD单层可以承受显著的应变,在这里,将拉曼光谱和光致发光光谱相结合,以表征通过CVD生长的一百多个MoS2单层样品中的应变。分析了声子的频率随应变的变化,并用于提取区域中心和边缘声子的Grüneisen参数。此外,讨论了缺陷引起的纵向声(LA)和横向声(TA)拉曼带的强度与应变和电子掺杂的关系。将获得的实验模式-Grüneisen参数与通过密度泛函理论(DFT)计算的参数进行比较,更好地表征应变类型及其对Grüneisen参数的影响。研究结果表明,使用拉曼光谱来确定2DMoS2中的缺陷密度必须始终考虑应变效应。据作者所知,这项工作构成了有关2D-MoS2中作为应变函数研究的双共振拉曼过程的第一份报告。从MoS2中的区域边缘声子获得Grüneisen参数的新方法也可以扩展到其他2D半导体TMD。
    The development of bottom-up synthesis routes for semiconducting transition metal dichalcogenides (TMDs) and the assessment of their defects are of paramount importance to achieve their applications. TMD monolayers grown by chemical vapor deposition (CVD) can be subjected to significant strain and, here, Raman and photoluminescence spectroscopies are combined to characterize strain in over one hundred MoS2 monolayer samples grown by CVD. The frequency changes of phonons as a function of strain are analyzed, and used to extract the Grüneisen parameter of both zone-center and edge phonons. Additionally, the intensity of the defect-induced longitudinal acoustic (LA) and transverse acoustic (TA) Raman bands are discussed in relation to strain and electronic doping. The experimental mode-Grüneisen parameters obtained are compared with those calculated by density functional theory (DFT), to better characterize the type of strain and its resulting effects on Grüneisen parameters. The findings indicate that the use of Raman spectra to determine defect densities in 2D MoS2 must be always conducted considering strain effects. To the best of the authors\' knowledge, this work constitutes the first report on double resonance Raman processes studied as a function of strain in 2D-MoS2. The new approach to obtain the Grüneisen parameter from zone-edge phonons in MoS2 can also be extended to other 2D semiconducting TMDs.
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  • 文章类型: Journal Article
    同立构聚(1-丁烯)(iPB)是一种有趣的半结晶热塑性材料,其特征在于具有出色的抗蠕变性和抗应力性,高韧性,刚度,和耐热性。这些独特的功能将iPB定位为特定应用的可行候选;然而,它的广泛使用受到某些固有局限性的阻碍。的确,iPB表现出复杂的多态行为,在老化过程中,动力学上有利的II型逐渐自发地转变为热力学上有利的I型,从而改变了材料的性能。尽管有潜力,获得具有极高分子量的iPB仍然难以捉摸,特别是当使用以其在丙烯聚合中的功效而闻名的均相催化剂时。在这项研究中,我们通过使用DFT计算对1-丁烯插入的区域选择性以及在主要(1,2)和次要(2,1)插入之后发生的终止反应进行建模,分析了控制1-丁烯聚合的机理方面。最后,还讨论了通过均相催化剂合成的iPB样品中导致4,1单元形成的异构化途径。所有这些方面,提供“旧”但仍然有趣的材料的主要缺点的机械图片。
    Isotactic poly (1-butene) (iPB) is an interesting semi-crystalline thermoplastic material characterized by notable physical and mechanical attributes encompassing superior creep and stress resistance, elevated toughness, stiffness, and thermal endurance. These distinctive features position iPB as a viable candidate for specific applications; however, its widespread utilization is hindered by certain inherent limitations. Indeed, iPB manifests an intricate polymorphic behavior, and the gradual and spontaneous transition of the kinetically favored form II to the thermodynamically favored form I during aging introduces alterations to the material\'s properties. Despite its potential, the attainment of iPB with an exceedingly high molecular mass remains elusive, particularly when employing homogeneous catalysts renowned for their efficacy in propene polymerization. In this study we analyze the mechanistic aspects governing 1-butene polymerization by using DFT calculations modelling the regioselectivity of 1-butene insertions and the termination reactions occurring after primary (1,2) and secondary (2,1) insertions. Finally, the isomerization pathways leading to the formation of 4,1 units in iPB samples synthesized by homogenous catalysts is also discussed. All these aspects, furnish a mechanistic picture of the main drawbacks of an \"old\" but still interesting material.
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