Co-reporter:Cheng Hou, Jingxing Jiang, Yinwu Li, Cunyuan Zhao, and Zhuofeng Ke
ACS Catalysis January 6, 2017 Volume 7(Issue 1) pp:786-786
Publication Date(Web):December 7, 2016
DOI:10.1021/acscatal.6b02505
Metal ligand cooperation (MLC) plays an important role in the development of homogeneous catalysts. Two major MLC modes have generally been proposed, known as the M-L bond mode and the (de)aromatization mode. To reveal the role of the dual potential functional sites on the MLC process, we present a detailed mechanistic study on a novel-designed Ru-PNNH complex possessing dual potential MLC functional sites for the M-L bond mode and the (de)aromatization mode, respectively. Our results indicate that the Ru-PNNH complex prefers the M-L mode exclusively during different stages of the catalytic cycle. The unusual double deprotonation process and the mechanistic preference are rationalized. The N-arm deprotonation is attributed to the small steric hindrance of the amido N-arm and the conjugation stabilization effect of the amido group. The origin of the unexpected exclusive mechanistic preference on the M-L bond mechanism is due to the conjugation effect of the amido group, which stabilizes the dearomatized complex and diminishes the driving force of the (de)aromatization mode. This study highlights the pivotal role of the ligand’s electronic effect on the MLC mechanism and should provide valuable information for the development of highly efficient bifunctional catalysts.Keywords: bifunctional; conjugation effect; metal ligand cooperation; ruthenium; steric effect;
Co-reporter:Xuepeng Zhang, Xueping Liu, David Lee Phillips, and Cunyuan Zhao
ACS Catalysis 2016 Volume 6(Issue 1) pp:248
Publication Date(Web):November 30, 2015
DOI:10.1021/acscatal.5b01735
The factors that influence the DNA nuclease activity of mononuclear facial copper complexes containing heterosubstituted cyclens were systematically investigated in this work using density functional theory (DFT) calculations. The heterosubstitution of cyclens were found to significantly affect the dimerization tendency of the mononuclear Cu(II) complexes examined and their respective pKa values of the metal-bonded water molecules. The Cu(II)–oxacyclen complex was found to be more favorable for the hydrolytic cleavage of the DNA dinucleotide analogue BNPP–(bis (p-nitrophenyl) phosphate). This was due to this species having a higher dimerization resistance to give rise to a higher concentration of the active catalyst and a lower pKa value of the Cu(II)-coordinated water molecule to facilitate an easier generation of the better nucleophile hydroxyl ion, which gave a lower reaction barrier. The dimerization of the Cu(I) complexes studied and their corresponding redox potentials were determined, and a remarkable reaction barrier was observed for the generation of a superoxide ROS (reactive oxygen species) mediated by the Cu(I)–oxacyclen complex. This behavior was attributed to the higher electronegativity of the O heteroatom, which facilitates the nucleophilic attack of the oxygen molecule and the Cu–O(OH2) bond fission via an enhancement of the Lewis acidity of the metal center and the formation of a significant hydrogen bond between the heterocyclic oxygen and the metal-bonded water molecule. The theoretical results reported here are in good agreement with the literature experimental observations and more importantly help to systematically elucidate the factors that influence the DNA nuclease activity of mononuclear facial copper complexes containing heterosubstituted cyclens in detail.Keywords: copper; cyclen; DFT; phosphoester; ROS
Co-reporter:Cheng Hou, Zhihan Zhang, Cunyuan Zhao, and Zhuofeng Ke
Inorganic Chemistry 2016 Volume 55(Issue 13) pp:6539
Publication Date(Web):June 20, 2016
DOI:10.1021/acs.inorgchem.6b00723
Metal ligand cooperation (MLC) catalysis is a popular strategy to design highly efficient transition metal catalysts. In this presented theoretical study, we describe the key governing factor in the MLC mechanism, with the Szymczak’s NNN-Ru and the Milstein’s PNN-Ru complexes as two representative catalysts. Both the outer-sphere and inner-sphere mechanisms were investigated and compared. Our calculated result indicates that the PNN-Ru pincer catalyst will be restored to aromatic state during the catalytic cycle, which can be considered as the driving force to promote the MLC process. On the contrary, for the NNN-Ru catalyst, the MLC mechanism leads to an unfavored tautomerization in the pincer ligand, which explains the failure of the MLC mechanism in this system. Therefore, the strength of the driving force provided by the pincer ligand actually represents a prerequisite factor for MLC. Spectator ligands such as CO, PPh3, and hydride are important to ensure the catalyst follow a certain mechanism as well. We also evaluate the driving force of various bifunctional ligands by computational methods. Some proposed pincer ligands may have the potential to be the new pincer catalysts candidates. The presented study is expected to offer new insights for MLC catalysis and provide useful guideline for future catalyst design.
Co-reporter:Xuepeng Zhang, Xueping Liu, David Lee Phillips and Cunyuan Zhao
Dalton Transactions 2016 vol. 45(Issue 4) pp:1593-1603
Publication Date(Web):08 Dec 2015
DOI:10.1039/C5DT03949E
The hydrolysis mechanisms of DNA dinucleotide analogue BNPP− (bis(p-nitrophenyl) phosphate) catalyzed by mononuclear/dinuclear facial copper(II) complexes bearing single alkyl guanidine pendants were investigated using density functional theory (DFT) calculations. Active catalyst forms have been investigated and four different reaction modes are proposed accordingly. The [Cu2(L1)2(μ-OH)]3+ (L1 is 1-(2-guanidinoethyl)-1,4,7-triazacyclononane) complex features a strong μ-hydroxo mediated antiferromagnetic coupling between the bimetallic centers and the corresponding more stable open-shell singlet state. Three different reaction modes involving two catalysts and a substrate were proposed for L1 entries and the mode 1 in which an inter-complex nucleophilic attack by a metal bound hydroxide was found to be more favorable. In the L3-involved reactions (L3 is 1-(4-guanidinobutyl)-1,4,7-triazacyclononane), the reaction mode in which an in-plane intracomplex scissoring-like nucleophilic attack by a Cu(II)-bound hydroxide was found to be more competitive. The protonated guanidine pendants in each proposed mechanism were found to play crucial roles in stabilizing the reaction structures via hydrogen bonds and in facilitating the departure of the leaving group via electrostatic attraction. The calculated results are consistent with the experimental observations that the Cu(II)–L3 complexes are hydrolytically more favorable than their L1-involved counterparts.
Co-reporter:Huiying Xu, Xuepeng Zhang, Zhuofeng Ke and Cunyuan Zhao
RSC Advances 2016 vol. 6(Issue 35) pp:29045-29053
Publication Date(Web):11 Mar 2016
DOI:10.1039/C5RA24340H
Dirhodium-contained catalysts mediated aliphatic C–H bond amination of aryl azides were studied using BPW91 functional. Calculations show the reactions with Rh2(esp)2 (esp = α,α,α′,α′-tetramethyl-1,3-benzenedipropionic acid) and the model compound Rh2(OCHO)4 as catalysts take place via similar mechanisms. Firstly, the dirhodium metal complex coordinates with the substrate and releases nitrogen gas. This rate-determining step results in the formation of the metal nitrene. Metal nitrene mediated intramolecular C–H bond amination is conducted via two alternative pathways, respectively. The singlet metal nitrene mediated intramolecular C–H bond amination occurs via a concerted and asynchronous pathway involving direct metal nitrene insertion into the C–H bond. The triplet metal nitrene case is a stepwise pathway involving a hydrogen transfer and then a diradical recombination. Our study suggests the triplet H-abstraction is more favorable than the singlet one. The resulted triplet intermediate would not go through the high-barrier diradical recombination process, but across to the singlet pathway via a MECP and form the final singlet product. The tethered esp ligands in Rh2(esp)2 provide steric effects to constrain the substrate-catalyst compound but indicates inconspicuous influence on the mechanisms of dirhodium catalyzed aliphatic C–H bond amination of aryl azides.
Co-reporter:Dr. Xuepeng Zhang;Dr. Huiying Xu;Xueping Liu;Dr. David Lee Phillips;Dr. Cunyuan Zhao
Chemistry - A European Journal 2016 Volume 22( Issue 21) pp:7288-7297
Publication Date(Web):
DOI:10.1002/chem.201600371
Abstract
The intramolecular benzylic C−H amination catalyzed by bimetallic paddlewheel complexes was investigated by using density functional theory calculations. The metal–metal bonding characters were investigated and the structures featuring either a small HOMO–LUMO gap or a compact SOMO energy scope were estimated to facilitate an easier one-electron oxidation of the bimetallic center. The hydrogen-abstraction step was found to occur through three manners, that is, hydride transfer, hydrogen migration, and proton transfer. The imido N species are more preferred in the Ru–Ru and Pd–Mn cases whereas coexisting N species, namely, singlet/triplet nitrene and imido, were observed in the Rh–Rh and Pd–Co cases. On the other hand, the triplet nitrene N species were found to be predominant in the Pd–Ni and Pd–Zn systems. A concerted asynchronous mechanism was found to be modestly favorable in the Rh–Rh-catalyzed reactions whereas the Pd–Co-catalyzed reactions demonstrated a slight preference for a stepwise pathway. Favored stepwise pathways were seen in each Ru–Ru- and Pd–Mn-catalyzed reactions and in the triplet nitrene involved Pd–Ni and Pd–Zn reactions. The calculations suggest the feasibility of the Pd–Mn, Pd–Co, and Pd–Ni paddlewheel complexes as being economical alternatives for the expensive dirhodium/diruthenium complexes in C−H amination catalysis.
Co-reporter:Ria Sanyal, Xuepeng Zhang, Priyanka Kundu, Tanmay Chattopadhyay, Cunyuan Zhao, Franz A. Mautner, and Debasis Das
Inorganic Chemistry 2015 Volume 54(Issue 5) pp:2315-2324
Publication Date(Web):February 19, 2015
DOI:10.1021/ic502937a
An “end-off” compartmental ligand has been synthesized by an abnormal Mannich reaction, namely, 2-[bis(2-methoxyethyl)aminomethyl]-4-isopropylphenol yielding three centrosymmetric binuclear μ-phenoxozinc(II) complexes having the molecular formula [Zn2(L)2X2] (Zn-1, Zn-2, and Zn-3), where X = Cl–, Br –, and I –, respectively. X-ray crystallographic analysis shows that the ZnO3NX chromophores in each molecule form a slightly distorted trigonal-bipyramidal geometry (τ = 0.55–0.68) with an intermetallic distance of 3.068, 3.101, and 3.083 Å (1–3, respectively). The spectrophotometrical investigation on their phosphatase activity established that all three of them possess significant hydrolytic efficiency. Michaelis–Menten-derived kinetic parameters indicate that the competitiveness of the rate of P–O bond fission employing the phosphomonoester (4-nitrophenyl)phosphate in 97.5% N,N-dimethylformamide is 3 > 1 > 2 and the kcat value lies in the range 9.47–11.62 s–1 at 298 K. Theoretical calculations involving three major active catalyst forms, such as the dimer-cis form (D-Cis), the dimer-trans form (D-Trans), and the monoform (M-1 and M-2), systematically interpret the reaction mechanism wherein the dimer-cis form with the binuclear-bridged hydroxide ion acting as the nucleophile and one water molecule playing a role in stabilizing the leaving group competes as the most favored pathway.
Co-reporter:Cheng Hou, Jingxing Jiang, Yinwu Li, Zhihan Zhang, Cunyuan Zhao and Zhuofeng Ke
Dalton Transactions 2015 vol. 44(Issue 37) pp:16573-16585
Publication Date(Web):13 Aug 2015
DOI:10.1039/C5DT02163D
The mimic of hydrogenases has unleashed a myriad of bifunctional catalysts, which are widely used in the catalytic hydrogenation of polar multiple bonds. With respect to ancillary ligands, the bifunctional mechanism is generally considered to proceed via the metal–ligand cooperation transition state. Inspired by the interesting study conducted by Hanson et al. (Chem Commun., 2013, 49, 10151), we present a computational study of a distinctive example, where a CoII-PNP catalyst with an ancillary ligand exhibits efficient transfer hydrogenation through a non-bifunctional mechanism. Both the bifunctional and non-bifunctional mechanisms are discussed. The calculated results, which are based on a full model of the catalyst, suggest that the inner-sphere non-bifunctional mechanism is more favorable (by ∼11 kcal mol−1) than the outer-sphere bifunctional mechanism, which is in agreement with the experimental observations. The origin of this mechanistic preference of the CoII-PNP catalyst can be attributed to its preference for the square planar geometry. A traditional bifunctional mechanism is less plausible for CoII-PNP due to the high distortion energy caused by the change in electronic configuration with the varied ligand field. Considering previous studies that focus on the development of ligands more often, this computational study indicates that the catalytic hydrogenation mechanism is controlled not only by the structure of the ligand but also by the electronic configuration of the metal center.
Co-reporter:Xianyan Xu, Jing Li, Xuepeng Zhang, Huiying Xu, Zhuo-Feng Ke and Cunyuan Zhao
RSC Advances 2015 vol. 5(Issue 28) pp:22135-22147
Publication Date(Web):18 Feb 2015
DOI:10.1039/C4RA13754J
Removing or reducing NO is meaningful for environment protection. Herein, the investigation of the probability of NO reduction on silicene is presented utilizing DFT calculations. Two mechanisms for NO reduction on silicene are provided: a direct dissociation mechanism and a dimer mechanism. The direct dissociation mechanism is characterized as the direct breaking of the N–O bond. The calculated potential energy surfaces show that the total energy barrier in the favored direct dissociation pathway is 0.466 eV. On the other hand, the dimer mechanism is identified to undergo a (NO)2 dimer formation on silicene, which then decomposes into N2O + Oad or N2 + 2Oad. The (NO)2 dimer formation on silicene is found to be feasible both in thermodynamics and kinetics. The formation energy barriers for (NO)2 dimer are lower than 0.231 eV. The calculation results indicate that the (NO)2 dimers can be readily reduced into N2O or N2. The energy barriers in the favored decomposition pathways to produce N2O are quite low (<0.032 eV). The energy barrier for the release of N2 is calculated to be 0.156 eV. The further reduction of N2O to N2 on silicene is also investigated. The results indicate it is easy to reduce N2O to N2 with an energy barrier of only 0.445 eV. NO reduction on silicene hence prefers to generate N2 via the dimer mechanism when compared to the direct dissociation. NO reduction on silicene with silicane as substrate is further proved to proceed via the same reduction mechanism as compared with the free-standing model. Hence, our results presented here suggest that silicene can be a potential material in NO removal, which will reduce NO into environmentally-friendly gases.
Co-reporter:Zhi-Feng Li, Hui-Xue Li, Xiao-Ping Yang, Xin-Wen Liu, Guo-Fang Zuo and Cunyuan Zhao
RSC Advances 2015 vol. 5(Issue 40) pp:31954-31964
Publication Date(Web):30 Mar 2015
DOI:10.1039/C5RA05458C
Direct coupling of unactivated alkynes and C(sp3)–H bonds catalyzed by a Pt(II, IV)-centered catalyst X (X = PtCl2, PtBr2, PtI2 and PtI4) (J. Am. Chem. Soc. 2009, 131, 16525) have been theoretically investigated with density functional theory (DFT). A comprehensive mechanistic DFT study of these reactions was carried out to better understand the experimental outcomes, and divergent and substrate-/catalyst-dependent mechanisms for the formation of ether derivatives were uncovered based on the computational results. Free energy diagrams for three types of mechanisms were computed, (a) in Mechanism I, the transition state implies a directed 1,5-hydrogen shift (pathways a1–a4), (b) Mechanism II leads to the formation of a Pt(II, IV) vinyl carbenoid (pathway b), and (c) Mechanism III involves an O-coordinated Pt and includes 5,6-hydrogen migration (pathway c). Results suggest that the catalytic mechanism with PtI4 is different to PtCl2, PtBr2 and PtI2 catalysts. When PtCl2, PtBr2 and PtI2 were used the insertion reaction pathway a2 is favored while PtI4 adopted the pathway a1. Comparing the energy profiles, the pathway a1 with PtI4 is the most favored. Through 1,5-hydrogen transfer, the concerted insertion pathway a1 with carbocationic intermediate is favored while the vinyl carbenoid mechanism is implausible.
Co-reporter:Xianyan Xu, Wei Ren, Huiying Xu, Xuepeng Zhang, Xiaowei Zheng, David Lee Phillips, Cunyuan Zhao
Sensors and Actuators B: Chemical 2015 213() pp: 139-149
Publication Date(Web):
DOI:10.1016/j.snb.2015.02.032
Co-reporter:Cheng Hou, Jingxing Jiang, Shidong Zhang, Guo Wang, Zhihan Zhang, Zhuofeng Ke, and Cunyuan Zhao
ACS Catalysis 2014 Volume 4(Issue 9) pp:2990
Publication Date(Web):July 28, 2014
DOI:10.1021/cs500688q
The hydrogenation of carbon dioxide catalyzed by half-sandwich transition metal complexes (M = Co, Rh, and Ir) was studied systematically through density functional theory calculations. All metal complexes are found to process a similar mechanism, which involves two main steps, the heterolytic cleavage of H2 and the hydride transfer. The heterolytic cleavage of H2 is the rate-determining step. The comparison of three catalytic systems suggests that the Ir catalyst has the lowest activation free energy (13.4 kcal/mol). In contrast, Rh (14.2 kcal/mol) and Co (18.3 kcal/mol) catalysts have to overcome relatively higher free energy barriers. The different catalytic efficiency of Co, Rh, and Ir is attributed to the back-donation ability of different metal centers, which significantly affects the H2 heterolytic cleavage. The highest activity of an iridium catalyst is attributed to its strong back-donation ability, which is described quantitatively by the second order perturbation theory analysis. Our study indicates that the functional group of the catalyst plays versatile roles on the catalytic cycle to facilitate the reaction. It acts as a base (deprotonated) to assist the heterolytic cleavage of H2. On the other hand, during the hydride transfer, it can also serve as Brønsted acid (protonated) to lower the LUMO of CO2. This ligand assisted pathway is more favorable than the direct attack of hydride to CO2. These finds highlight that the unique features of the metal center and the functional ligands are crucial for the catalyst design in the hydrogenation of carbon dioxide.Keywords: carbon dioxide; catalytic mechanism; cobalt; density functional theory; hydrogenation; iridium; metal effect; rhodium
Co-reporter:Xuepeng Zhang, Yajie Zhu, Xiaowei Zheng, David Lee Phillips, and Cunyuan Zhao
Inorganic Chemistry 2014 Volume 53(Issue 7) pp:3354-3361
Publication Date(Web):March 21, 2014
DOI:10.1021/ic402717x
The hydrolysis mechanisms of phosphor-monoester monoanions NPP– (p-nitrophenyl phosphate) catalyzed by unsymmetrical bivalent dinuclear complexes are explored using DFT calculations in this report. Four basic catalyst–substrate binding modes are proposed, and two optional compartments for the location of the nucleophile-coordinated metal center are also considered. Five plausible mechanisms are examined in this computational study. Mechanisms 1, 2, and 3 employ an unsymmetrical dizinc complex. All three mechanisms are based on concerted SN2 addition–substitution pathways. Mechanism 1, which involves more electronegative oxygen atoms attached to the imine nitrogen atoms in the nucleophile-coordinated compartment, was found to be more competitive compared to the other two mechanisms. Mechanisms 4 and 5 are based on consideration of the substitution of the bivalent metal centers and the intrinsic flexibility of the ligand. Both mechanisms 4 and 5 are based on stepwise SN2-type reactions. Magnesium ions with hard base properties and more available coordination sites were found to be good candidates as a substitute in the MII dinuclear phosphatases. The reaction energy barriers for the more distorted complexes are lower than those of the less distorted complexes. The proper intermediate distance and a functional second coordination sphere lead to significant catalytic power in the reactions studied. More importantly, the mechanistic differences between the concerted and the stepwise pathways suggest that a better nucleophile with more available coordination sites (from either the metal centers or a functional second coordination sphere) favors concerted mechanisms for the reactions of interest. The results reported in the paper are consistent with and provide a reasonable interpretation for experimental observations in the literature. More importantly, our present results provide some practical suggestions for the selection of the metal centers and how to approach the design of a catalyst.
Co-reporter:Xuepeng Zhang, Yajie Zhu, Hui Gao, and Cunyuan Zhao
Inorganic Chemistry 2014 Volume 53(Issue 22) pp:11903-11912
Publication Date(Web):October 31, 2014
DOI:10.1021/ic501084a
The solvolysis mechanisms of RNA phosphodiester model 2-(hydroxypropyl)-4-nitrophenyl phosphate (HpPNP) catalyzed by mononuclear zinc(II) complexes are investigated in the paper via a theoretical approach. The general-base-catalyzed (GBC) and specific-base-catalyzed (SBC) mechanisms are thoroughly discussed in the paper, and the calculations indicate a SBC mechanism (also named as the direct nucleophilic attack mechanism) when the cyclization of HpPNP is promoted by the Zn:[12]aneN3 complex ([12]aneN3 = 1,5,9-triazacyclododecane). The ligand effect is considered by involving two different catalysts, and the results show that the increasing size catalyst provides a lower energy barrier and a significant mechanistic preference to the SBC mechanism. The solvent medium effect is also explored, and reduced polarity/dielectric constant solvents, such as light alcohols methanol and ethanol, are more favorable. Ethanol is proven to be a good solvent medium because of its low dielectric constant. The computational results are indicative of concerted pathways. Our theoretical results are consistent with and well interpret the experimental observations and, more importantly, provide practical suggestions on the catalyst design and selection of reaction conditions.
Co-reporter:Xuepeng Zhang;Xianyan Xu;Huiying Xu;Xiting Zhang; Dr. David Lee Phillips; Dr. Cunyuan Zhao
ChemPhysChem 2014 Volume 15( Issue 9) pp:1887-1898
Publication Date(Web):
DOI:10.1002/cphc.201301216
Abstract
Density functional calculations are utilized to explore the hydrolysis mechanisms of the phosphomonoester 4-nitrophenyl phosphate catalyzed by a symmetrical zinc(II) complex. The formation process and properties of the active catalyst are verified. Eight plausible mechanisms are proposed and categorized into three groups. All of the proposed mechanisms, except for Mechanism 7 (see text), are SN2-type addition–substitution reaction pathways. Nucleophilic attack at the ortho position occurs in Mechanism 7 with a relatively high reaction barrier. Mechanisms 1 and 2 in the monocatalyst model, Mechanisms 5 to 7 in the sandwich-dual-catalyst model, as well as the nucleophilic addition–substitution step in Mechanism 8 are concerted reaction pathways, whereas the rest appear to occur in a stepwise manner. Meanwhile, the explicit solvent model is utilized to consider direct hydrogen bonds and solvation interactions and these results indicate that the added water molecule is involved in the hydrolysis process, but does not change the mechanisms significantly. Mechanism 8, with the lowest reaction barrier, is the most favored reaction pathway of the eight proposed mechanisms, although Mechanisms 1, 4, and 6 are in competition with Mechanism 8. In consideration of the zinc(II) complex concentration, Mechanism 1 is only the predominant reaction pathway at a low zinc(II) complex concentration; Mechanisms 4 and 6 tend to be more competitive with increasing concentration of the zinc(II) complexes, and Mechanism 8 is favored at high zinc(II) complex concentrations. Our calculated results are consistent with, and can be used to systematically interpret, experimental observations. More importantly, insightful suggestions are made regarding the catalyst design and selection of the reaction environment.
Co-reporter:Xuepeng Zhang, Huiying Xu, and Cunyuan Zhao
The Journal of Organic Chemistry 2014 Volume 79(Issue 20) pp:9799-9811
Publication Date(Web):September 25, 2014
DOI:10.1021/jo5019987
The reaction mechanisms and chemoselectivity on the intramolecular allylic C–H amination versus alkene aziridination of 4-pentenylsulfamate promoted by four elaborately selected dirhodium paddlewheel complexes are investigated by a DFT approach. A predominant singlet concerted, highly asynchronous pathway and an alternative triplet stepwise pathway are obtained in either C–H amination or alkene aziridination reactions when mediated by weak electron-donating catalysts. A singlet stepwise C–H amination pathway is obtained under strongly donating catalysts. The rate-determining step in the C–H amination is the H-abstraction process. The subsequent diradical-rebound C–N formation in the triplet pathway or the combination of the allylic carbocation and the negative changed N center in the singlet pathway require an identical energy barrier. A mixed singlet–triplet pathway is preferred in either the C–H insertion or alkene aziridination in the Rh2(NCH3CHO)4 entry that the triplet pathway is initially favorable in the rate-determining steps, and the resultant triplet intermediates would convert to a singlet reaction coordinate. The nature of C–H amination or alkene aziridination is estimated to be a stepwise process. The theoretical observations presented in the paper are consistent with the experimental results and, more importantly, provide a thorough understanding of the nature of the reaction mechanisms and the minimum-energy crossing points.
Co-reporter:Huiying Xu, Xiting Zhang, Zhuo-Feng Ke, Zhi-Feng Li, Xian-Yan Xu, Cheng-Yong Su, David Lee Phillips and Cunyuan Zhao
RSC Advances 2013 vol. 3(Issue 38) pp:17131-17142
Publication Date(Web):22 Jul 2013
DOI:10.1039/C3RA42168F
The mono- and bis-cyclopropanation of allenamides with the zinc carbenoid Zn(CH2Cl)2 have been studied using density functional theory calculations employing the M06 functional. The monomeric and dimeric precursor complexes were both constructed to model the reaction processes. In the monomeric reaction, the formation of the endo-monocyclopropyl species takes place via a methylene transfer pathway rather than a carbometalation pathway. The formation of the exo-monocyclopropyl species does not readily occur via a methylene transfer pathway due to a high activation barrier. The corresponding carbometalation pathway was not able to be found. Following the monocyclopropanation step, the biscyclopropanation of the endo-monocyclopropyl species is facile to form amidospiro[2.2]pentane. In the aggregation model, the allenamides and the zinc carbenoid form a dimer aggregate that is then followed by two pathways. One pathway takes place via transition states inside the aggregate structure (denoted here as a closed-mode process) while the other pathway introduces another zinc carbenoid molecule from outside the aggregation species (denoted here as an open-mode process). The aggregate mechanisms are not favored because the dimeric reactant of the open-mode process is not stable to coexist with the monomer and the activation barriers of the two aggregate pathways are higher than those of the monomeric pathways. The calculation results show that the key factors in the reaction mechanisms are the co-planarity of the allenic moiety with the oxazolidinone ring, the torsional strain in the butterfly-type transition state, the ring strain in the substrate–carbenoid complexes and the coordination between the carbenoid-Zn and O(CO) atoms and other long-distance interactions.
Co-reporter:Xiting Zhang, Zhuofeng Ke, Nathan J. DeYonker, Huiying Xu, Zhi-Feng Li, Xianyan Xu, Xuepeng Zhang, Cheng-Yong Su, David Lee Phillips, and Cunyuan Zhao
The Journal of Organic Chemistry 2013 Volume 78(Issue 24) pp:12460-12468
Publication Date(Web):November 26, 2013
DOI:10.1021/jo402101h
The mechanisms and enantioselectivities of the dirhodium (Rh2L4, L = formate, N-methylformamide, S-nap)-catalyzed intramolecular C–H aminations of 3-phenylpropylsulfamate ester have been investigated in detail with BPW91 density functional theory computations. The reactions catalyzed by the Rh2II,II catalysts start from the oxidation of the Rh2II,II dimer to a triplet mixed-valent Rh2II,III–nitrene radical, which should facilitate radical H-atom abstraction. However, in the Rh2(formate)4-promoted reaction, as a result of a minimum-energy crossing point (MECP) between the singlet and triplet profiles, a direct C–H bond insertion is postulated. The Rh2(N-methylformamide)4 reaction exhibits quite different mechanistic characteristics, taking place via a two-step process involving (i) intramolecular H-abstraction on the triplet profile to generate a diradical intermediate and (ii) C–N formation by intersystem crossing from the triplet state to the open-shell singlet state. The stepwise mechanism was found to hold also in the reaction of 3-phenylpropylsulfamate ester catalyzed by Rh2(S-nap)4. Furthermore, the diradical intermediate also constitutes the starting point for competition steps involving enantioselectivity, which is determined by the C–N formation open-shell singlet transition state. This mechanistic proposal is supported by the calculated enantiomeric excess (94.2% ee) with the absolute stereochemistry of the product as R, in good agreement with the experimental results (92.0% ee).
Co-reporter:Xuepeng Zhang, Hui Gao, Huiying Xu, Jianqiao Xu, Hui Chao, Cunyuan Zhao
Journal of Molecular Catalysis A: Chemical 2013 Volumes 368–369() pp:53-60
Publication Date(Web):March 2013
DOI:10.1016/j.molcata.2012.11.025
Density functional theory (DFT) calculations were used to explore the hydrolysis mechanism of the DNA analog BNPP (BNPP = bis(4-nitrophenyl)phosphate) catalyzed by the mononuclear zinc(II):OH− complex of 1,5,9-triazacyclododecane (Zn:([12] aneN3)). We present a binding mode in which one terminal phosphoryl oxygen atom as well as the nucleophilic group (hydroxyl anion) binds to zinc center. Two potential mechanisms were found as follows: one is a concerted mechanism with a reaction barrier of 18.1 kcal/mol in liquid phase of implicit solvent and 13.8 kcal/mol in liquid phase of explicit solvent of water molecules; the other is a stepwise mechanism with a hydroxylated phosphate reaction intermediate of a quasi-trigonal bipyramid configuration but is less feasible. Both the concerted reaction pathway and stepwise reaction pathway are SN2 manner of nucleophilic substitution reactions. Meanwhile polar protic solvents like water, methanol and ethanol are favored in the catalyst-assisted hydrolysis mechanism. We explore the rationality of deprotonation of mono-anionic phosphates in the transient products and find that it is difficult to dissociate a proton and the ultimate product is NPP− rather than NPP2−. These results are consistent with and systematically interpret the experimental observations, more importantly, provide useful suggestions in the catalyst design and solvent selection.Graphical abstractHighlights► The hydrolysis of phosphodiester catalyzed by zinc complex was explored. ► A stepwise pathway and a concerted pathway were found and the latter is favored. ► The two mechanisms are SN2 manner of nucleophilic substitution reactions. ► Polar protic solvents are favorable in the catalyst-assisted SN2 reaction. ► The phosphate in the product would not dissociate a proton at neutral pH solution.
Co-reporter:Hanlu Wang, Nathan J. De Yonker, Hui Gao, David Lee Phillips, Cunyuan Zhao, Liangnian Ji and Zong-Wan Mao
RSC Advances 2012 vol. 2(Issue 20) pp:7849-7859
Publication Date(Web):13 Jun 2012
DOI:10.1039/C2RA20984E
The thermodynamics and kinetics for the binding of the potential anticancer complex [(η6-benz)Ru(en)(H2O)]2+ (benz = benzene, en = ethylenediamine) (1) to nucleotides under neutral and acidic conditions were studied by density functional theory (DFT) calculations, employing 5′-guanosine monophosphate (5′-GMP) and 5′-adenosine monophosphate (5′-AMP) as model reactants. Based on the different binding modes, there were four pathways located for each nucleotide, two stepwise (a and b) and two concerted (c and d). In line with experiments, the reaction first proceeded with the binding of the 5′-phosphate group, and then underwent a slow intramolecular rearrangement to the N7 purine binding products. For 5′-GMP, concerted pathways are also possible based on our calculated results. The reaction of 5′-GMP is faster under acidic conditions than under neutral conditions. However, for the reaction of 5′-AMP, the first step of the phosphate binding is apparently more facile in a neutral environment than in an acidic one. Due to the thermodynamic sink of the phosphate bound intermediates, the second step of the intramolecular rearrangement from phosphate to A(N7)-binding exhibited a prohibitively high free energy of activation under neutral conditions. An approximately 9 kcal mol−1 difference in the reaction between 5′-GMP and 5′-AMP shows a clear preference for the binding of 5′-GMP over 5′-AMP, in agreement with experimental observation. It was also revealed that the phosphate as a hydrogen bond acceptor played an important role in the interaction of the Ru–arene complexes with nucleotides.
Co-reporter:Hanlu Wang;Nathan J. DeYonker;Xiting Zhang
Journal of Molecular Modeling 2012 Volume 18( Issue 10) pp:4675-4686
Publication Date(Web):2012 October
DOI:10.1007/s00894-012-1467-3
The piano-stool RuII arene complex [(η6-benz)Ru(bpm)(py)]2+ (benz = benzene, bpm = 2,2′-bipyrimidine, and py = pyridine), which is conventionally nonlabile (on a timescale and under conditions relevant for biological reactivity), can be activated by visible light to selectively photodissociate the monodentate ligand (py). In the present study, the aquation and binding of the photocontrolled ruthenium(II) arene complex [(η6-benz)Ru(bpm)(py)]2+ to various biomolecules are studied by density functional theory (DFT) and time-dependent DFT (TDDFT). Potential energy curves (PECs) calculated for the Ru–N (py) bonds in [(η6-benz)Ru(bpm)(py)]2+ in the singlet and triplet state give useful insights into the photodissociation mechanism of py. The binding energies of the various biomolecules are calculated, which allows the order of binding affinities among the considered nuleic-acid- or protein-binding sites to be discerned. The kinetics for the replacement of water in the aqua complex with biomolecules is also considered, and the results demonstrate that guanine is superior to other biomolecules in terms of coordinating with the RuII aqua adduct, which is in reasonable agreement with experimental observations.
Co-reporter:Hanlu Wang, Nathan J. DeYonker, Hui Gao, Liangnian Ji, Cunyuan Zhao, Zong-Wan Mao
Journal of Organometallic Chemistry 2012 704() pp: 17-28
Publication Date(Web):
DOI:10.1016/j.jorganchem.2011.12.034
Co-reporter:Zhi-Feng Li, Yanzhong Fan, Nathan J. DeYonker, Xiting Zhang, Cheng-Yong Su, Huiying Xu, Xianyan Xu, and Cunyuan Zhao
The Journal of Organic Chemistry 2012 Volume 77(Issue 14) pp:6076-6086
Publication Date(Web):July 2, 2012
DOI:10.1021/jo300849t
The mechanism and intermediates of hydroalkylation of aryl alkynes via C(sp3)–H activation through a platinum(II)-centered catalyst are investigated with density functional theory at the B3LYP/[6-31G(d) for H, O, C; 6-31+G(d,p) for F, Cl; SDD for Pt] level of theory. Solvent effects on reactions were explored using calculations that included a polarizable continuum model for the solvent (THF). Free energy diagrams for three suggested mechanisms were computed: (a) one that leads to formation of a Pt(II) vinyl carbenoid (Mechanism A), (b) another where the transition state implies a directed 1,4-hydrogen shift (Mechanism B), and (c) one with a Pt-aided 1,4-hydrogen migration (Mechanism C). Results suggest that the insertion reaction pathway of Mechanism A is reasonable. Through 4,5-hydrogen transfer, the Pt(II) vinyl carbenoid is formed. Thus, the stepwise insertion mechanism is favored while the electrocyclization mechanism is implausible. Electron-withdrawing/electron-donating groups substituted at the phenyl and benzyl sp3 C atoms slightly change the thermodynamic properties of the first half of Mechanism A, but electronic effects cause a substantial shift in relative energies for the second half of Mechanism A. The rate-limiting step can be varied between the 4,5-hydrogen shift process and the 1,5-hydrogen shift step by altering electron-withdrawing/electron-donating groups on the benzyl C atom. Additionally, NBO and AIM analyses are applied to further investigate electronic structure changes during the mechanism.
Co-reporter:Fenglei Cao, Wei Ren, Xianfang Xu, Ye-Xiang Tong, Cunyuan Zhao
Chemical Physics Letters 2011 Volume 512(1–3) pp:81-86
Publication Date(Web):16 August 2011
DOI:10.1016/j.cplett.2011.07.010
Abstract
Metallocenes can be encapsulated inside the carbon nanotubes. The structural, energetic and electronic properties of organometallic MCp2@SWCNT are obtained from DFT method. We verify that such encapsulation is noncovalent functionalization, and examined binding energies and charge transfers of MCp2@(16, 0)SWCNT systems. Consistent with recent experimental findings, the optimal distance between FeCp2 center and near tube-wall is 4.7 (5.1) Å for the configuration where MCp2’s fivefold axis is parallel (vertical) to nanotube axis, while the minimal diameter is 9.4 (10.2) Å to exothermically encapsulate FeCp2 molecules. Finally we clarify the doping effects near the band gap by encapsulations of CoCp2 and NiCp2.
Co-reporter:Juping Wang, Huiying Xu, Hui Gao, Cheng-Yong Su, Cunyuan Zhao and David Lee Phillips
Organometallics 2010 Volume 29(Issue 1) pp:42-51
Publication Date(Web):December 15, 2009
DOI:10.1021/om900371u
Density functional theory (DFT) calculations at the B3LYP/6-31G(d,p) (LANL2DZ for Zr) level of theory were performed to elucidate the reaction mechanism for the reduction of amides to aldehydes using Cp2Zr(H)Cl as a reducer. In particular, a detailed study was done that involved a proposed iminium cation species in the reaction mechanism. Our calculations suggest the first step of the reaction is the insertion of the C═O moiety into Zr−H through an “inside” mode of action that leads to the formation of a Zr−O intermediate that has been observed in previously reported experiments. Under anhydrous conditions, the cleavage of the O−C bond of the Zr−O intermediate results in the formation of an iminium cation, but this process is both kinetically and thermodynamically unfavorable. Nevertheless, under hydrous conditions, the cleavage of the O−C bond of the Zr−O intermediate leads to the formation of a highly active iminium cation intermediate, and this process occurs with the assistance of water hydrogen bonding. This step is also the rate-determining step, and the activation energy was determined to be 19.8 kcal/mol. Subsequently a water molecule attacks the iminium cation to produce an amine intermediate. Finally, the water-catalyzed elimination reaction occurs to yield the aldehyde product. Water hydrogen bonding plays an important role in assisting the cleavage of the O−C and the C−N bonds during the reaction. The above reaction mechanism indicates that the sources of the aldehyde-group oxygen and the hydrogen in the aldehyde product are H2O and Cp2Zr(H)Cl, respectively, which is consistent with the experimental observations of Georg and co-workers.
Co-reporter:Fenglei Cao, Xianyan Xu, Wei Ren and Cunyuan Zhao
The Journal of Physical Chemistry C 2010 Volume 114(Issue 2) pp:970-976
Publication Date(Web):December 16, 2009
DOI:10.1021/jp910025y
The adsorption/dissociation of the O2 molecule on the surface of silicon carbide nanotubes (SiCNTs) was investigated by density functional theory. We found several adsorption configurations, including chemisorption and cycloaddition configurations, for triplet and singlet O2. Unlike the case for carbon nanotubes, the chemisorption of triplet O2 on SiCNTs is exothermic with remarkable charge transfer from nanotubes to the O2 molecule. Singlet O2 adsorption on the surface of SiCNTs can yield cycloaddition structures with large binding energies and sizable charge transfer. The reaction mechanism studies show that for triplet O2, the chemisorption configuration is favorable, but the cycloaddition configuration is preferred for singlet O2. For singlet O2, we also studied the dissociation of the O2 molecule, and a two-step mechanism was presented. The dissociation of molecular O2 results in formation of two three-membered rings with large binding energies. The key to the dissociation process of singlet O2 on the SiCNT surface is the first step with a barrier energy of 0.40 eV. Finally, the electronic properties of SiCNTs with adsorbed triplet and singlet O2 are shown to be dramatically influenced.
Co-reporter:Zhen Guo, Jiadan Xue, Zhuofeng Ke, David Lee Phillips and Cunyuan Zhao
The Journal of Physical Chemistry B 2009 Volume 113(Issue 18) pp:6528-6532
Publication Date(Web):April 9, 2009
DOI:10.1021/jp8104584
A computational study was done for the reactions of the 2-fluorenylnitrenium ion (2FN) with guanosine (G) and its monohydrate tautomer (G·H2O) to form the key N7 or C8 intermediates that may then proceed to produce the C8 adduct product. The 2FN + G·H2O reactions with the transition state of the C8 pathway being noticeably lower than that of the N7 pathway are very different from those found for the 2FN + G reactions where the transition states for the N7 pathway are lower than those for the C8 pathway. This is due to the lone pair of N7 being protected by hydrogen bonding in a protic solvent (G·H2O in our case), so the C8 position of guanosine will become more nucleophilic than position N7. Computational results for the 2FN + G·H2O reactions predict that the C8 intermediate, rather than the N7 intermediate, is the predominant intermediate formed from the reaction. Our results are consistent with time-resolved absorption and time-resolved resonance Raman experiments that found a very fast reaction of 2FN with guanosine to produce a “C8 intermediate” with a common time constant for the decay of 2FN and the formation of the C8 intermediate. The results here suggest that explicit hydrogen-bonding effects on the chemical reactivity of guanosine may contribute to arylnitrenium ions reacting with guanine derivatives to produce predominantly C8 adducts rather than N7 adducts.
Co-reporter:Ran Fang, Cheng-Yong Su, Cunyuan Zhao and David Lee Phillips
Organometallics 2009 Volume 28(Issue 3) pp:741-748
Publication Date(Web):January 7, 2009
DOI:10.1021/om800751u
The mechanism and regioselectivity of gold(I)-catalyzed synthesis of highly substituted furans based on 1-(1-alkynyl)cyclopropyl ketones with nucleophiles have been investigated using density functional theory calculations done at the BH and HLYP/6-31G(d, p) (SDD for Au) level of theory. Solvent effects on these reactions have been explored by calculations that included a polarizable continuum model (PCM) for the solvent (dichloromethane). Our calculations suggest that the first step of the cycle is the cyclization of the carbonyl oxygen onto the triple bond to form a new and stable five-membered resonance structure of an oxonium ion and a carbocation intermediate. Furthermore, the seven-membered carbocation intermediate proposed by Zhang and Schmalz was found and characterized as a transition structure on the potential energy surface. The attack of the carbonyl oxygen to the gold-coordinated alkynes results in the formation of a resonance structure intermediate, which upon subsequent trapping with alcohols followed by migration of a hydrogen atom results in the formation of the final products and regeneration of the catalyst. The key reaction step is the attack of the oxygen atom of the CH3OH on the C−C σ bond of the cyclopropane moiety to yield new organogold intermediates through formation of a C−O bond and cleavage of a C−C bond. The cleavage of the C−C bond is strongly favored kinetically in the case of the C1−C2 bond and required only 19.8 kcal/mol of energy, while the activation energy for cleavage of the C1−C3 bond was found to be 31.8 kcal/mol and indicates that the ring-opening cycloisomerization for cyclopropyl ketones has high regioselectivity. Our computational results are consistent with the experimental observations of Zhang and Schmalz for the gold(I)-catalyzed synthesis of highly substituted furans based on 1-(1-alkynyl)cyclopropyl ketones with nucleophiles.
Co-reporter:Zhen Guo, Zhuofeng Ke, David Lee Phillips and Cunyuan Zhao
Organometallics 2008 Volume 27(Issue 2) pp:181-188
Publication Date(Web):December 27, 2007
DOI:10.1021/om7007452
Density functional theory (DFT) calculations were performed to investigate the quintet, triplet, and singlet potential energy surfaces associated with the C-H activation of methane by laser-ablated molybdenum (Mo) atoms recently observed experimentally by Andrews and co-workers. The present computational study aims to better understand the nature of the reaction mechanisms for C-H activation by Mo atoms. The processes for activation of methane by the excited Mo atoms appear to produce CH3—MoH, CH2═MoH2, and CH≡MoH3 complexes. The crossing seams between the potential energy surfaces and possible spin inversion processes for the direct conversion of methane to a high oxidation state transition metal complex that contains a carbon-metal double or triple bond are examined using the intrinsic reaction coordinate (IRC) approach. The minimum energy reaction pathway is found to involve spin inversion three times in different reaction steps. In total, three spin states (quintet, triplet, and singlet) are involved in going from the entrance channel to the exit channel: 5Mo + CH4 → CH3—MoH (51) → CH2═MoH2 (32) → CH≡MoH3 (13). The first crossing seam exists prior to TS1–2, a three-centered transition state for the H-transfer of complex 1 to form a double carbon-metal bond complex 2. This crossing seam is a key aspect in the reaction pathway because the molecular system should change its spin multiplicity from the quintet state to the triplet state near this crossing region, which leads to a significant decrease in the barrier height of TS1–2 from 51.0 to 33.8 kcal mol−1 at the B3LYP level of theory. The second crossing seam between the quintet potential energy surface (PES) and the singlet PES is found not to play a significant role because the triplet potential energy surface lies significantly below the quintet and singlet potential energy surfaces. Accordingly, the molecular system would preferentially move on the triplet potential energy surfaces before encountering the second seam. The crossing seam between the triplet exit channel and the singlet exit channel can take place, in which complex 13 containing a triple carbon-metal bond is formed via an H-transfer process. This crossing seam will again lead to a spin inversion from the triplet to the singlet state, and this leads to a large decrease in the height of the reaction barrier from 40.8 to 17.2 kcal mol−1.
Co-reporter:Zhiwei Li, Cunyuan Zhao, Liuping Chen
Journal of Molecular Structure: THEOCHEM 2008 Volume 854(1–3) pp:46-53
Publication Date(Web):15 April 2008
DOI:10.1016/j.theochem.2007.12.032
The equilibrium geometries, electronic structures, harmonic vibrational frequencies, and nucleus independent chemical shifts (NICS) of Bi5-, Bi5M (M = Li, Na, K), and Bi5M+ (M = Be, Mg, Ca) clusters are calculated by the density functional theory (DFT) method. Our calculation show that the ground states of Bi5-, Bi5M, and Bi5M+ species are predicted to be the D5h, C5v, and C5v structures, respectively. In addition, the Bi5- unit preserves its structural and electronic integrity in forming the Bi5M and Bi5M+ complexes. Molecular orbital analysis and NICS show that the planar Bi5- (D5h) anion satisfies the Hükcel rule of 4n + 2 π electrons and magnetic criteria for aromaticity with six delocalized π electrons and negative NICS values. The dissected NICS suggests that the aromaticity of Bi5- (D5h) arise primarily from the contributions of Bi–Bi σ bonds and Bi–Bi π bonds, while the aromaticity of Bi5M and Bi5M+ mainly owe to the Bi–Bi σ bonds.
Co-reporter:Zhao-Hui Li, Zhi-Yuan Geng, Cunyuan Zhao, Yong-Cheng Wang, Le-Yan Liu
Journal of Molecular Structure: THEOCHEM 2007 Volume 807(1–3) pp:173-178
Publication Date(Web):1 April 2007
DOI:10.1016/j.theochem.2006.12.034
The cyclopropanation reaction of ethene with aluminum carbenoid has been studied by means of the B3LYP hybrid density functional method. The reaction goes through two pathways: methylene transfer and carbometalation. In methylene transfer pathway, a quantum-chemical investigation shows that the reactions of the carbenoids X2AlCH2X 1-X, (X = F, Cl, Br, I) with ethene 2 to cyclopropane 3 + lX3 profit from a weakening of the C–X bonds by the C–Al bonds in the carbenoids 1-X and in the complex [1-X∗2]. The C–F bond is more affected than the C–I bond. Since in the transition states 3[1-X∗2]‡ AlHal is strongly decomplexed, the cleavage of the C–Hal bond is essential compensated by the formation of the Al–Hal bonds, which leads to almost equal transition state energy for the reactions of 1-X with 2. In contrast with methylene transfer, the cyclopropanation reaction of the carbometalation pathway profit from a weakening of the C–Al bonds by the C–X bonds.
Co-reporter:Zhiwei Li, Cunyuan Zhao, Liuping Chen
Journal of Molecular Structure: THEOCHEM 2007 Volume 807(1–3) pp:17-23
Publication Date(Web):1 April 2007
DOI:10.1016/j.theochem.2006.12.002
The equilibrium geometries, electronic structures, harmonic vibrational frequencies, and nucleus independent chemical shifts (NICS) of Sb5- and Sb5M (M = Li, Na, and K) clusters are calculated by the density functional theory (DFT) method. Our calculation show that the Sb5- species has the aromatic planar cyclic D5h structure and the Sb5M species have the pyramidal C5v structures as the ground states, and the Sb5- unit preserves its structural and electronic integrity in forming the Sb5M complexes. Molecular orbital analysis and NICS show that the planar Sb5- anion satisfies the Hükcel rule of 4n + 2π electrons and magnetic criteria for aromaticity with six delocalized π electrons and negative NICS values. The dissected NICS suggests that the aromaticity of Sb5-(D5h) and Sb5M (C5v) arise primarily from the contributions of Sb–Sb π bonds, Sb–Sb σ bonds, and the NICS distributions and contributions, and their changing tendencies of the Sb5M (C5v) species are similar to the isolated Sb5-(D5h) anion.
Co-reporter:Zhuofeng Ke;Yubing Zhou;Hui Gao Dr.;David Lee Phillips Dr.
Chemistry - A European Journal 2007 Volume 13(Issue 23) pp:
Publication Date(Web):16 MAY 2007
DOI:10.1002/chem.200700145
An investigation into the mechanism and stereochemistry of chiral lithium-carbenoid-promoted cyclopropanation reactions by using density functional theory (DFT) methods is reported. Previous work suggested that this type of cyclopropanation reaction may proceed by competition between a methylene-transfer mechanism and a carbometalation mechanism. In this paper, it is demonstrated that the intramolecular cyclopropanation reactions promoted by chiral carbenoids 1 and 2 proceed by the methylene-transfer mechanism. The carbometalation mechanism was found to have a much higher reaction barrier and does not appear to compete with the methylene-transfer mechanism. The Lewis base group does not enhance the carbometalation pathway enough to compete with the methylene-transfer pathway. The present computational results are consistent with experimental observations for these cyclopropanation reactions. The factors governing the stereochemistry of the intramolecular cyclopropanation reaction by the methylene-transfer mechanism were examined to help elucidate the origin of the stereoselectivity observed in experiments. Both the directing group and the configuration at the C1 centre were found to play a key role in the stereochemistry. Carbenoid 1 has a chiral C1 centre of R configuration. The Lewis base group directs the cyclization of carbenoid 1 to form a single product. In contrast, the Lewis base group cannot direct the cyclization of carbenoid 2 to furnish a stereoselective product due to the S configuration of the chiral C1 centre in carbenoid 2. This relationship of the stereochemistry to the chiral character of the carbenoid has implications for the design of new efficient carbenoid reagents for stereoselective cyclopropanation.
Co-reporter:Zhiwei Li, Cunyuan Zhao, Liuping Chen
Journal of Molecular Structure: THEOCHEM 2007 Volume 809(1–3) pp:45-54
Publication Date(Web):14 May 2007
DOI:10.1016/j.theochem.2007.01.010
The equilibrium geometries, vibrational frequencies, adiabatic energy separations for the ground and several excited states of XAl3 (X = Si, Ge, Sn, Pb) and their positive and negative ions have been investigated by the DFT level, followed by the CCSD(T) level for further energy refining, and the vertical detachment energies (VDE) for XAl3- are computed and compared with the experiment and other theoretical calculations by outer valence Green function (OVGF). On the basis of our computed excited states energy separations, we have successfully suggested assignments for the observed X, A, and B states in the anion photoelectron spectra of XAl3-. The assignments of the excited states are consistent excellently with the experimental excitation energies and the previous OVGF method generally. The canonical MO–NICS analysis suggest that the π and σ MOs of the XAl3- (C2v) clusters both contribute to their aromaticity, and the π MOs contribute mostly.
Co-reporter:Zhiwei Li, Cunyuan Zhao, Liuping Chen
Journal of Molecular Structure: THEOCHEM 2007 Volume 810(1–3) pp:1-6
Publication Date(Web):25 May 2007
DOI:10.1016/j.theochem.2007.01.032
The equilibrium geometries, energies, harmonic vibrational frequencies, and nucleus-independent chemical shifts (NICS) of the new type sandwich structures [P4MP4]n− (M = Ti, V, Cr, Mn, Fe, Co, and Ni; n = 0, 1 or 2) are researched at the B3LYP/6-311G∗ and B3PW91/6-311G∗ levels of theory. The calculations reveal that the Ti, V, Cr, and Mn species adopt the eclipsed (D4h) conformations, while the Fe, Co, and Ni analogs adopt the staggered (D4d) conformations as their stable structures, and once the sandwich complexes are formed, the P42- square properties remain unchanged. The NICS calculations confirm that the P42- ring in the Ti, V, Cr, and Mn species exhibit σ and π antiaromaticity, while it exhibit σ and π aromaticity in the Fe, Co, and Ni analogs.
Co-reporter:Xuepeng Zhang, Xiaowei Zheng, David Lee Phillips and Cunyuan Zhao
Dalton Transactions 2014 - vol. 43(Issue 43) pp:NaN16299-16299
Publication Date(Web):2014/08/06
DOI:10.1039/C4DT01491J
Density functional theory (DFT) was utilized to investigate the hydrolysis reaction mechanisms of phosphodiester BNPP (BNPP = bis(4-nitrophenyl)phosphate) catalyzed by a symmetrical oxyimine-based macrocyclic dinuclear zinc(II) complex. We examined the nature of the nucleophilic reagent and the active form of the catalyst. The coordination and binding models of the catalyst–substrate complex were explored and we investigated two catalyst configurations (a ridge configuration and a plane configuration), four basic catalyst–substrate binding models (a mono-point-binding model, a dual-point-binding model, an OH-bridging model and a mono-center-dual-binding model) and two alternate roles for the metal-coordinated hydroxide ion (whether it acts as a nucleophile or as a general base to facilitate the deprotonation of a solvent molecule). The one-point-binding mode was found to be preferred to construct a starting reactant. Nine plausible reaction mechanisms were proposed and investigated. Mechanism 1, a stepwise SN2-type addition–substitution reaction involving a para-position nucleophilic attack and the configuration inversion of the phosphate, was found to be the most favorable pathway. All of the proposed pathways are derived from alternate mechanisms such as a ping-pong mechanism and an AP mechanism. The ping-pong mechanism in combination with the role of the metal-coordinated hydroxide ion acting as a nucleophile was found to be more competitive than the other mechanisms examined. Results reported in this paper are consistent with, and can be utilized to systematically interpret, the experimental observations in the literature.
Co-reporter:Cheng Hou, Jingxing Jiang, Yinwu Li, Zhihan Zhang, Cunyuan Zhao and Zhuofeng Ke
Dalton Transactions 2015 - vol. 44(Issue 37) pp:NaN16585-16585
Publication Date(Web):2015/08/13
DOI:10.1039/C5DT02163D
The mimic of hydrogenases has unleashed a myriad of bifunctional catalysts, which are widely used in the catalytic hydrogenation of polar multiple bonds. With respect to ancillary ligands, the bifunctional mechanism is generally considered to proceed via the metal–ligand cooperation transition state. Inspired by the interesting study conducted by Hanson et al. (Chem Commun., 2013, 49, 10151), we present a computational study of a distinctive example, where a CoII-PNP catalyst with an ancillary ligand exhibits efficient transfer hydrogenation through a non-bifunctional mechanism. Both the bifunctional and non-bifunctional mechanisms are discussed. The calculated results, which are based on a full model of the catalyst, suggest that the inner-sphere non-bifunctional mechanism is more favorable (by ∼11 kcal mol−1) than the outer-sphere bifunctional mechanism, which is in agreement with the experimental observations. The origin of this mechanistic preference of the CoII-PNP catalyst can be attributed to its preference for the square planar geometry. A traditional bifunctional mechanism is less plausible for CoII-PNP due to the high distortion energy caused by the change in electronic configuration with the varied ligand field. Considering previous studies that focus on the development of ligands more often, this computational study indicates that the catalytic hydrogenation mechanism is controlled not only by the structure of the ligand but also by the electronic configuration of the metal center.
Co-reporter:Xuepeng Zhang, Xueping Liu, David Lee Phillips and Cunyuan Zhao
Dalton Transactions 2016 - vol. 45(Issue 4) pp:NaN1603-1603
Publication Date(Web):2015/12/08
DOI:10.1039/C5DT03949E
The hydrolysis mechanisms of DNA dinucleotide analogue BNPP− (bis(p-nitrophenyl) phosphate) catalyzed by mononuclear/dinuclear facial copper(II) complexes bearing single alkyl guanidine pendants were investigated using density functional theory (DFT) calculations. Active catalyst forms have been investigated and four different reaction modes are proposed accordingly. The [Cu2(L1)2(μ-OH)]3+ (L1 is 1-(2-guanidinoethyl)-1,4,7-triazacyclononane) complex features a strong μ-hydroxo mediated antiferromagnetic coupling between the bimetallic centers and the corresponding more stable open-shell singlet state. Three different reaction modes involving two catalysts and a substrate were proposed for L1 entries and the mode 1 in which an inter-complex nucleophilic attack by a metal bound hydroxide was found to be more favorable. In the L3-involved reactions (L3 is 1-(4-guanidinobutyl)-1,4,7-triazacyclononane), the reaction mode in which an in-plane intracomplex scissoring-like nucleophilic attack by a Cu(II)-bound hydroxide was found to be more competitive. The protonated guanidine pendants in each proposed mechanism were found to play crucial roles in stabilizing the reaction structures via hydrogen bonds and in facilitating the departure of the leaving group via electrostatic attraction. The calculated results are consistent with the experimental observations that the Cu(II)–L3 complexes are hydrolytically more favorable than their L1-involved counterparts.
![[2,2'-Bipyridin]-6-amine, N-[bis(1,1-dimethylethyl)phosphino]-](/data/chemimg/3721100/1415800-79-1.png)
![[2,2'-Bipyridin]-6-amine, N-[bis(1,1-dimethylethyl)phosphino]-](/data/chemimg/3721100/1415800-79-1_b.png)
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![2,2'-Bipyridine, 6-[[bis(1,1-dimethylethyl)phosphino]methylene]-1,6-dihydro-](/data/chemimg/3721300/1942949-76-9_b.png)
![Benzene, 1-bromo-4-[(4-fluorophenyl)sulfonyl]-](http://img.cochemist.com/ccimg/400/383-28-8.png)
![Benzene, 1-bromo-4-[(4-fluorophenyl)sulfonyl]-](http://img.cochemist.com/ccimg/400/383-28-8_b.png)
![1-[(R)-PHENYL(1-PIPERIDINYL)METHYL]-2-NAPHTHOL](http://img.cochemist.com/ccimg/400/312-31-2.png)
![1-[(R)-PHENYL(1-PIPERIDINYL)METHYL]-2-NAPHTHOL](http://img.cochemist.com/ccimg/400/312-31-2_b.png)
![Ruthenium,[6-[[bis(1,1-dimethylethyl)phosphino-kP]methylene]-N,N-diethyl-1,6-dihydro-2-pyridinemethanaminato-kN1,kN2]carbonylhydro-, (SP-5-52)-](http://img.cochemist.com/ccimg/864000/863971-63-5.png)
![Ruthenium,[6-[[bis(1,1-dimethylethyl)phosphino-kP]methylene]-N,N-diethyl-1,6-dihydro-2-pyridinemethanaminato-kN1,kN2]carbonylhydro-, (SP-5-52)-](http://img.cochemist.com/ccimg/864000/863971-63-5_b.png)
![Rhodium, bis[m-[a,a,a',a'-tetramethyl-1,3-benzenedipropanoato(2-)-kO1,kO'3:kO3,kO'1]]di-, (Rh-Rh)](http://img.cochemist.com/ccimg/819100/819050-89-0.png)
![Rhodium, bis[m-[a,a,a',a'-tetramethyl-1,3-benzenedipropanoato(2-)-kO1,kO'3:kO3,kO'1]]di-, (Rh-Rh)](http://img.cochemist.com/ccimg/819100/819050-89-0_b.png)
![BENZO[F]QUINOLINE-1,3-DICARBOXYLIC ACID](http://img.cochemist.com/ccimg/63400/63359-38-6.png)
![BENZO[F]QUINOLINE-1,3-DICARBOXYLIC ACID](http://img.cochemist.com/ccimg/63400/63359-38-6_b.png)
![4-[[(8r,9s,13s,14s)-13-methyl-17-oxo-7,8,9,11,12,14,15,16-octahydro-6h-cyclopenta[a]phenanthren-3-yl]oxy]-4-oxobutanoic Acid](http://img.cochemist.com/ccimg/58600/58534-72-8.png)
![4-[[(8r,9s,13s,14s)-13-methyl-17-oxo-7,8,9,11,12,14,15,16-octahydro-6h-cyclopenta[a]phenanthren-3-yl]oxy]-4-oxobutanoic Acid](http://img.cochemist.com/ccimg/58600/58534-72-8_b.png)
