Dezhan Chen

On the mechanism of carbonyl hydrogenation catalyzed by iron catalyst.

Density functional theory calculations have been performed to investigate the detailed mechanism of the carbonyl hydrogenation catalyzed by the first well-defined bifunctional iron catalyst. The catalytic reaction proceeds by hydrogen transfer and dihydrogen activation. The hydrogen transfer reaction occurs via the bifunctional mechanism in which the two hydrogen atoms attached on the Fe and O of the catalyst are transferred to the oxygen and carbon atom of the carbonyl compound concertedly. Both the alcohol-mediated and nonalcohol-mediated dihydrogen activation processes are explored.

Enantioselectivity in organocatalytic cascade double Michael addition reaction: a theoretical study.

We have investigated important intermediates and key transition states of the organocatalyzed cascade double Michael addition using density functional theory. The calculated results suggest that the reaction contains intermolecular nucleophilic addition and intramolecular cyclization, both involving the formation of two stereocenters. The iminium-enamine catalysis of secondary amine unit enables the cascade addition to proceed consecutively. As an electron transport, the iminium attracts the electron stream to promote the nucleophilic addition. Then enamine causes the electron stream to catalyze the cyclization. As H bond donor, the catalyst forms three types of C-H···O H bond with substrates. The enantioselectivity and diastereoselectivity are dominated by the catalyst backbone. Two group links of pyrrole-phenyl and pyrrole-silyl ether orient the reaction in paths with smaller rotations of the linked single bonds. Our conclusion is supported by NBO analysis and the predicted ee, dr values according to the experiment.

Density Functional Theory Study of Rh(III)-Catalyzed C–H Activations and Intermolecular Annulations between Benzamide Derivatives and Allenes

Density functional theory has been applied to gain insight into the Cp*Rh(OAc)2-catalyzed C-H activation and intermolecular annulation of benzamide derivatives with allenes. The study shows that the reactions proceed in three steps: (1) C-H activation induced by Rh catalyst reacting with benzamide derivatives, (2) carborhodation of allene, and (3) regeneration of Rh catalyst. The results indicate that the N-H deprotonation makes the following C-H activation much easier. The regio- and stereoselectivities of 1a (N-pivaloyloxy benzamide)/2a (cyclohexylallene) and 1b (N-pivaloyloxy-4-methyl-benzamide)/2b (1,1-dimethyl allene) depend on the allene carborhodation step. The steric hindrance effect is the dominant factor. We also discuss the reaction mechanism of 1c (N-methoxy benzamide)/2a. The chemoselectivity between 1c/2a is determined by the N-O cleavage step. Replacement of OPiv by OMe leads to loss of the stabilization effect provided by C=O in OPiv. Additionally, Cp*Rh(OAc)(OPiv) is produced in the Cp*Rh(OAc)2 regeneration step, which can work as catalyst as well.

Retracted article: Enantioselectivity of aza-MBH-type reaction of nitroalkene to N-tosylimine catalyzed by thiourea-tertiary amine: a theoretical study

We, the named authors, hereby wholly retract this RSC Advances article. Signed: Nan Lu, Lin Meng, Dezhan Chen and Guiqiu Zhang, China, February 2012. Retraction endorsed by Sarah Ruthven, Managing Editor. Retraction published 1st February 2012.

Tandem Synthesis of Pyrrolo[2,3-b]quinolones via Cadogen-Type Reaction

A tandem [3 + 2] cycloaddition/reductive cyclization of nitrochalcones with activated methylene isocyanides for the efficient synthesis of pyrrolo[2,3-b]quinolones is reported. In this reaction, the in situ generated dihydropyrroline acts as the internal reductant to convert the nitro into an electrophilic nitroso group, which undergoes subsequent C-N bond formation. Transition-metal-free, simple experimental procedure and ready accessibility of starting materials characterize the present transformation.

Theoretical characterization of the conformational features of unnatural oligonucleotides containing a six nucleotide genetic alphabet

The addition of the unnatural P:Z base pair to the four naturally occurring DNA bases expands the genetic alphabet and yields an artificially expanded genetic information system (AEGIS). Herein, the structural feature of oligonucleotides containing a novel unnatural P:Z base pair is characterized using both molecular dynamics and quantum chemistry. The results show that the incorporation of the novel artificial base pair (P:Z) preserves the global conformational feature of duplex DNA except for some local structures. The Z-nitro group imparts new properties to the groove width, which widens the major groove. The unnatural oligonucleotides containing mismatched base pairs exhibit low stability. This ensures efficient and high-fidelity replication. In general, the incorporation of the P:Z pair strengthens the stability of the corresponding DNA duplex. The calculated results also show that the thermostability originates from both hydrogen interaction and stacking interaction. The Z-nitro group plays an important role in enhancing the stability of the H-bonds and stacking strength of the P:Z pair. Overall, the present results provide theoretical insights in the exploration of artificially expanded genetic information systems.

Theoretical investigation of hydrogen bonding between water and platinum(II): an atom in molecule (AIM) study

Recently, Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] [1] reported a hydrogen-bonding-like interaction between a water molecule and a d8 metal ion (PtII) based on neutron diffraction, and provided the first crystallographic evidence for this interaction. We studied the hydrogen bonding of the O–H ··· Pt interaction theoretically using atoms in molecule (AIM) and natural bond orbital analysis (NBO) in the crystallographic geometries. The method used density functional theory (DFT) with the hybrid B3LYP function. For platinum atoms, we used the Los Alamos National Laboratory 2-Double-Zeta (LANL2DZ) basis set, and for the other atoms we used 6-311++G(d,p) basis sets. Criteria based on a topological analysis of the electron density were used in order to characterize the nature of interactions in the complexes. The main purpose of the present work is to provide an answer to the following questions: Why can a filled d orbital of square-planar d8 metal ions such as platinum(II) also act as hydrogen-bond acceptors? Can a study based on the electron charge density answer this question? A good correlation between the density at the intermolecular bond critical point and the energy interaction was found. The interaction is mainly closed-shell and there is some charge transfer in this system.

Insight into the Bonding Mechanism and the Bonding Covalency in Noble Gas–Noble Metal Halides: An NBO/NRT Investigation

The bonding between noble gas and noble metal halide like hydrogen bonding (H-bonding) motivates us to investigate the bonding mechanism and the bonding covalency in NgMX (Ng = He, Ne, Ar, Kr, Xe, Rn; M = Cu, Ag, Au; X = F, Cl, Br, I) complexes using natural bond orbital (NBO) and natural resonance theory (NRT) methods. In this study, we introduce the new resonance bonding model in H-bonding into NgMX bonding. We provide strong evidence for resonance bonding involving two important resonance structures: Ng: M-X ↔ Ng+-M :X- in each of NgMX complexes, originating in the nNg → σ*MX hyperconjugative interaction. The covalency of the bonding could be understood by the localized nature of Ng-M bonds in these two resonance structures, and the degree of Ng-M covalency can be quantitatively described by calculated NRT bond orders bNgM. Furthermore, we find that the bond order satisfies conservation of bond order, bNgM + bMX = 1, for all of the studied complexes. On the basis of the conservation of bond order and some statistical correlations, we also reveal that the Ng-M bond (except He-Ag and Ne-Ag bonds) can be tuned by changing the auxiliary ligand X. Overall, the present studies provide new insight into the bonding mechanism and the covalency of the bonding in noble gas-noble metal halides, and develop one resonance bonding model.

Electron density characteristics and charge transfer effect of hydrogen bond O–H···Pt(II): atoms in molecules study and natural bond orbital analysis

In this report, we extended the works of Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] on the nature of O–H···Pt hydrogen bond in trans-[PtCl2(NH3)(N–glycine)]·H2O(1·H2O) complex, by computational study of O–H···Pt interaction in [NBu4][Pt(C6F5)3(8-hydroxyquinaldine)], with emphasis on charge transfer effect in this interaction of platinum(II) and hydrogen atom. According to the crystallographic geometry reported by José María Casas et al., [NBu4][Pt(C6F5)3(8-hydroxyquinaldine)] possesses one O–H···Pt hydrogen bridging interaction, similar to the case in trans-[PtCl2(NH3)(N–glycine)]·H2O(1·H2O) complex. On the basis of topological criteria of electron density, we characterised this O–H···Pt interaction. Charge transferred between platinum(II) and σ*O–H orbital in this complex was calculated by using NBO method. The stabilised energy associated to charge transfer was estimated using a direct proportionality, that is 2–3 eV per electron transferred. Charge transfer effects in O–H···Pt hydrogen bonds were studied for these two complexes. Our results indicate that the interaction of O–H···Pt is closed–shell in nature with significant charge transfer, and that charge transfer effect is not negligible in the interaction of O–H···Pt. The second conclusion is different from the result of Rizzato et al.

The stabilizing effect of the transient imine directing group in the Pd(II)-catalyzed C(sp3)–H arylation of free primary amines

A transient directing group (DG) has been successfully applied to assist the activation of C–H bonds. In this paper, we have performed density functional theory (DFT) calculations to investigate the mechanism of ligand-assisted Pd(II)-catalyzed C(sp3)–H arylation. In the presence of a quinoline-8-carbaldehyde (ArQCHO) ligand, the reaction starts with the nucleophilic addition of 2-butylamine with the ligand to generate the transient imine DG, which binds to the Pd(II) center via bidentate coordination. The sequential C(sp3)–H activation, oxidative addition of [Ph2I]+ with a palladacycle, and C–C reductive elimination yield the final product of arylation. Instead of the traditional inner-sphere concerted metalation deprotonation (CMD) mechanism, a novel deprotonation mechanism for the rate-determining C(sp3)–H activation is discovered; that is, the methyl group is deprotonated by an outer-sphere pivalate. A comparison with the results of the reaction without the ligand indicates that the square planar geometry formed by the transient DG with Pd(II) significantly reduces the distortion energies, which ultimately makes the C(sp3)–H activation kinetically favorable.