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The underlying discrimination mechanism and the origins of catalyst-dependent selectivity are disclosed for divergent cycloaddition reactions.

A novel mechanism of the arylation of arenes via norbornene (NBE) relay palladation through meta- to para-selectivity was revealed via density functional theory (DFT) calculations. Our calculated results revealed that the reaction was initiated by a [mono-N-protected amino acid ligand (MPAA)–Pd] complex to activate at first the meta-C–H guided by the directing group (DG), and para-arylation was subsequently achieved by NBE relay palladation from meta- to para-position. Significantly, the palladium/norbornene (Pd/NBE) cooperative catalysis was catalyzed by a Pd–Ag bimetallic complex, which accounted for the experimental fact that no yield detected without Ag. The reaction pathway through para- to meta-selectivity was also investigated, while this pathway was kinetically unfavorable. The results revealed that the initial DG guided C–H site activation was the rate-determining step and played an important role in determining site-selectivity. The primary meta-activation was favorable in energy due to the less ring strain in the cyclic nitrile-coordinated C–H transition states in the meta position. Moreover, the perfect cooperation of a remote directing template and a transient mediator NBE through the alternating association with the Pd center achieved the relay through meta- to para-position. The present results provide a reasonable insight into the para-C–H arylation by the Pd/MPAA/NBE cooperative catalysis in conjunction with a precise DG and Ag(I) additive.

This article presents an exploration of stereospecificity and divergent reactivity of Pd-catalyzed α,α-disubstituted alkenyl hydrazones to synthesize 1,4-dienes in the

Transition metal-catalyzed three-component reactions of arenes, dienes, and carbonyls enable the convergent synthesis of homoallylic alcohols. Controlling regioselectivity is a central challenge for the difunctionalization of substituted 1,3-dienes in which multiple unbiased C═C bonds exist. Here, the mechanisms of Cp*Co(III)-catalyzed three-component C-H bond addition to terpenes and formaldehydes were investigated by density functional theory calculations. The reaction proceeds via sequential C(sp2)-H activation, migratory insertion, β-hydride elimination, hydride reinsertion, and C-C bond formation to yield the final product. The migratory insertion is the rate- and regioselectivity-determining step of the overall reaction. We employed an energy decomposition approach to quantitatively dissect the contributions of different types of interactions to regioselectivity. For the 2-alkyl substituted 1,3-dienes, the orbital interactions in the 3,4-insertion are intrinsically more favorable as compared to that in the 4,3-insertion, while the stronger steric effects between metallacycle and 1,3-diene override the intrinsic electronic preference. However, the steric effects failed to rationalize the unfavorable 1,2-insertion that is analogous to 4,3-insertion and even bears smaller steric effects. The donor-acceptor interaction analysis indicates that orbital interactions between σCo-C and πC═C decreased significantly in the 1,2-insertion transition state, which leads to higher activation energy barriers. These insights into the dominant effects controlling regioselectivity will enable rational design of new catalysts for selective functionalization of dienes.

CO2 hydrogenation into value-added chemicals not only offer an economically beneficial outlet but also help reduce the emission of greenhouse gases. Herein, the density functional theory (DFT) studies have been carried out on CO2 hydrogenation reaction for formamide production catalyzed by two different N–H ligand types of PNP iron catalysts. The results suggest that the whole mechanistic pathway has three parts: (i) precatalyst activation, (ii) hydrogenation of CO2 to generate formic acid (HCOOH), and (iii) amine thermal condensation to formamide with HCOOH. The lower turnover number (TON) of a bifunctional catalyst system in hydrogenating CO2 may attribute to the facile side-reaction between CO2 and bifunctional catalyst, which inhibits the generation of active species. Regarding the bifunctional catalyst system addressed in this work, we proposed a ligand participated mechanism due to the low pKa of the ligand N–H functional in the associated stage in the catalytic cycle. Remarkably, catalysts without the N–H ligand exhibit the significant transfer hydrogenation through the metal centered mechanism. Due to the excellent catalytic nature of the N–H ligand methylated catalyst, the N–H bond was not necessary for stabilizing the intermediate. Therefore, we confirmed that N–H ligand methylated catalysts allow for an efficient CO2 hydrogenation reaction compared to the bifunctional catalysts. Furthermore, the influence of Lewis acid and strong base on catalytic N-formylation were considered. Both significantly impact the catalytic performance. Moreover, the catalytic activity of PNMeP-based Mn, Fe and Ru complexes for CO2 hydrogenation to formamides was explored as well. The energetic span of Fe and Mn catalysts are much closer to the precious metal Ru, which indicates that such non-precious metal catalysts have potentially valuable applications.

The 3d transition metal-catalyzed enantioselective C–H functionalization provides a sustainable strategy for the construction of chiral molecules. A better understanding of the catalytic nature of the reactions and the factors controlling the enantioselectivity is important for rational design of more efficient systems. Herein, the mechanisms of Ni-catalyzed enantioselective C–H cyclization of imidazoles are investigated by density functional theory (DFT) calculations. Both the π-allyl nickel(ii)-promoted σ-complex-assisted metathesis (σ-CAM) and the nickel(0)-catalyzed oxidative addition (OA) mechanisms are disfavored. In addition to the typically proposed ligand-to-ligand hydrogen transfer (LLHT) mechanism, the reaction can also proceed via an unconventional σ-CAM mechanism that involves hydrogen transfer from the JoSPOphos ligand to the alkene through P–H oxidative addition/migratory insertion, C(sp2)–H activation via σ-CAM, and C–C reductive elimination. Importantly, computational results based on this new mechanism can indeed reproduce the experimentally observed enantioselectivities. Further, the catalytic activity of the π-allyl nickel(ii) complex can be rationalized by the regeneration of the active nickel(0) catalyst via a stepwise hydrogen transfer, which was confirmed by experimental studies. The calculations reveal several significant roles of the secondary phosphine oxide (SPO) unit in JoSPOphos during the reaction. The improved mechanistic understanding will enable design of novel enantioselective C–H transformations., Several unique reactivity patterns of the Ni/JoSPOphos manifold, including facile hydrogen transfer via the two-step oxidative addition/migratory insertion and C(sp2)–H activation via an unconventional σ-CAM mechanism, were disclosed in this work.

We synthesized and characterized three types of isostructural iodoargentates, [TM(phen)3]Ag2I4·3DMF (TM = Co (1), Ni (2), Zn (3)), [TM(phen)3]Ag3I5·DMF (TM = Co (4), Ni (5), Zn (6)), and [TM(phen)3...

A vital challenge in designing optical and redox-active receptors lies in coupling a specific recognition center with a valid response system to facilitate multi-feature detection. Herein, we present a reaction-type receptor, which incorporates the ferrocenyl group into the rhodamine B fluorophore via a well-defined acylthiourea bridge, for the multi-model analysis of Hg2+ in water and living cells. This receptor was successfully used to efficiently detect Hg2+ in an aqueous medium by chromogenic, fluorogenic, and electrochemical assessments and exhibited a low detection limit (1.60 × 10−8 M) and fast response time (

In recent years, the versatile reactivity of Cu-catalyzed hydrocarbonylative coupling of alkynes with alkyl halides has drawn widespread attention. In this paper, we explore in detail the origin of different regioselectivities for terminal/internal alkynes coupling with primary, secondary and tertiary alkyl halides by using density functional theory (DFT) calculations. The present results reveal that the dominant factor of high Cα-regioselectivity in alkyne insertion is mainly the electron effect for the terminal alkyne, in which the higher electron density of terminal carbon makes electrophilic attack more favorable. For internal alkynes, such as 1-phenyl-1-hexyne, the d orbital in Cu which is able to conjugate with the HOMO of the benzene ring plays a dominant role in Cα-selective formation of alkenyl copper. Moreover, we also confirmed that enones were formed by C–C concerted coupling of alkenyl copper with acyl bromide instead of the oxidative addition suggested in the literature. Notably, the origin of the regioselectivity of 1,2-reduction over 1,4-reduction is mainly the steric effect, whether for the terminal alkyne or the internal alkyne case.

A computational mechanistic study has been performed on Pd(II)-catalyzed enantioselective reactions involving acetyl-protected aminomethyl oxazolines (APAO) ligands that significantly improved reac...

The mechanisms of aminocarbonylations and alkoxycarbonylations in coupling of aminophenols with iodoarenes catalyzed by the bidentate phosphorus ligand Pd complexes were explored with theoretical calculations. The origins of chemoselective carbonylation mediated by ligands and bases were disclosed. According to our calculations, the bifurcation points of reaction pathways caused by different ligands and bases combinations are

The mechanism of rhodium(III)-catalyzed C H functionalization of o-vinylphenols (1a) with alkynes has been investigated with DFT calculations. The results suggest the whole reaction is comprised with four stages: (I) O H deprotonation, (II) C H activation induced by Rh(III) catalyst interacting with o-vinylphenols, (III) alkyne coordination and (IV) regeneration of Rh(III) catalyst. The C H activation step proceeds under the concerted metalation deprotonation mechanism. The regioselectivity and chemoselectivity of the reaction also have been discussed, respectively. The regioselectivity for different C H activation sites is depended on the coordination structure of the related Rh(III) complex. In addition, when the substrates are substituted with alkyl (or alkenes) at the terminal position of the alkene, such as (E)-2-(prop-1-en-1-yl)phenol 1b and 2-allylphenol 1c, the apparent activation energies (ΔG) are obviously higher than that of 1a, which indicates that they are unfavorable to occur. The effect of CO2Me substituent on the para position to the hydroxyl (1d) is also investigated.

Using metal complexes and organic species together to synergistically catalyze reactions is of great interest to the chemical community. However, the mechanism of stereodivergent dual catalysis, especially the role of each catalyst, is elusive. In this paper, mechanistic details for stereodivergent coupling of aldehydes and alkynes via synergistic catalysis of rhodium and amine were explored using density functional theory calculations. The synergistic roles of each catalyst, and the origin of the regioselective and enantioselective stereodivergent coupling for the reaction are disclosed. The results show that two substrates are activated independently at first by rhodium and amine so that a Rh–π-allyl complex and enamine are generated. The combination of two activated intermediates provides access to the divergent stereocenters through an outer sphere mechanism. Rhodium catalyst predominates, not only in the activation of substrates, but also in the control of regioselectivity and enantioselectivity. The Rh–π-allyl complex regulates the molecular skeleton and each transition state is controlled by the outer sphere via an enamine–phosphate hydrogen bond. Thus, the energy barriers of the reaction are significantly reduced to 11.1 kcal mol−1via synergistic catalysis of metal complexes and organic amines. The calculated ee and de values are in very good agreement with the experimental results.

Directing groups (DGs) are widely employed to enhance the selectivity and reactivity of C–H activation. In this work, to illustrate the effects of mono- and bi-dentate DGs, we systematically explored the Ni(0)-catalyzed annulation of an aromatic amide containing N,N-bidentate or monodentate amide nitrogen DG with alkyne through density functional theory (DFT) calculations. For an amide featuring bidentate 2-pyridinylmethylamine DG, the proposed mechanism involves oxidative addition of the N–H bond, alkyne insertion into Ni–H, C(sp2)–H activation via concerted metalation deprotonation (CMD), alkyne insertion into Ni–C(sp2) and reductive elimination. However, under the same reaction conditions, the oxidative addition of the N–H bond utilizing the monodentate amide NH DG is unfavorable, due to the lack of a distal N(sp2) coordination site. Deportation of amide NH by a strong base allows the amidate anion to coordinate with the metal center, and the catalytic cycle involves oxidative addition of the C(sp2)–H bond, sequential alkyne insertion into the Ni–H and Ni–C bonds and reductive elimination. The significant difference between the two reactions is the C–H activation process; that is, C–H cleavage occurs via the CMD mechanism in the bidentate DG while oxidative addition in the monodentate DG. The sequence of alkyne insertion and the structural trans effect of the hydride were also deeply investigated.

Recycle of thorium is an essential process in the thorium-uranium closed fuel cycle of molten salt reactor (MSR). Pyrochemical treatment of spent nuclear fuel using chloride molten salts as medium has been considered as a promising method. In this article, we performed molecular dynamics simulations on the ThCl4 LiCl molten salts using a polarizable force field parameterized by us from first-principles calculations. The microscopic structures and macroscopic properties at different compositions were investigated using the developed force field to understand the structure/property relationship in the mixture. The differences between ThCl4 LiCl and ThF4 LiF MSs are compared to understand the behaviors of Th4+ in the fluoride-chloride mixed media. In the molten fluorides, the coordination number of Th4+ is larger, and the resulting more shared anions lead to lower ThF dissociation barrier and shorter lifetime of the Th4+ first solvation shell. Our results also indicate the Pauling's structural rules for crystals can be used to rationalize the local structures in molten salts. © 2018 Wiley Periodicals, Inc.

A computational study of Cp*CoIII/RhIII-catalyzed carboamination/olefination of N-phenoxyacetamides with alkenes was carried out to elucidate the catalyst-controlled chemoselectivity. The reaction ...

A RhIII -catalysed three-component synthesis of isoindolinone frameworks via direct assembly of benzoyl chlorides, o-aminophenols and activated alkenes has been developed. The process involves in situ generation of o-aminophenol (OAP)-based bidentate directing group (DG), RhIII -catalysed tandem ortho C-H olefination and subsequent cyclization via aza-Michael addition. This protocol exhibits good chemoselectivity and functional group tolerance. Computational studies showed that the presence of hydroxyl group on the N-aryl ring could enhance the chemoselectivity of the reaction.

The mechanism of B(C6F5)3 promoted Cp*CoIII-catalyzed C–H functionalization was investigated in detail employing density functional theory (DFT). The formation free energy of every possible species in the multicomponent complex system was explored and the optimal active catalyst was screened out. The results uncover the role of B(C6F5)3 played in forming active catalyst is from the coordination with OAc–, but not from the formation of [I(C6F5)3B]−, and no acceleration effect is found in C–H activation as well as the formation of CoIII-carbene intermediate. Moreover, present theoretical results elucidate the Cp*CoIII-catalyzed C–H activation is mediated by imine N-coordination other than general proposed the sequence of N-deprotonation directed C–H activation. The metal-controlled C–H/N–H selectivity was then elucidated by insighting into [Cp*CoIIIOAc]+/[Cp*RhIIIOAc]+-catalyzed C–H and N–H activations, respectively.

Mechanistic details of the decarbonylation of unstrained ketones by (IMesMe)Ni and (IMesMe)NiCO complexes with a N-heterocyclic carbene ligand (IMesMe) have been explored by density functional theory calculations. The calculated mechanism sheds light on the origin of realization for the decarbonylation catalytic cycle. (IMesMe)Ni mediates the first decarbonylation cycle and generates a biaryl product and (IMesMe)NiCO, which is inactive for the substrate 4-methyl-4′-trifluoromethyl benzophenone 1. However, (IMesMe)NiCO can mediate the decarbonylation of 3-quinolinyl ketone 2 and realize the catalytic cycle. The decarbonylation step is the rate-determining step controlling whether the transformation can be mediated catalytically. The stabilization energy E(2) of BDC(O)–C(methyl phenyl) → LVNi for the decarbonylation transition state plays a dominant role in the catalytic cycle. In addition, an electron-withdrawing group on the arene can stabilize the orbital energies facilitating the initial C–C(O) oxidative addition step. A moderate linear correlation is observed between the oxidative addition barriers and the charges transferred from (IMesMe)Ni to the benzoyl moiety.

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.

The detailed mechanism of palladium-catalyzed γ-C(sp3)-H olefination/cyclization of triflyl-protected amines was investigated by density functional theory (DFT) calculations. The olefinated intermediate was initially formed in the first catalytic cycle involving ligand exchange, bicarbonate-assisted C(sp3)-H bond cleavage, alkene insertion and 'reductive β-hydride elimination'. The following syn-addition and reductive elimination furnish the aza-Wacker product. The first step of reductive elimination is the rate-determining step. The mechanism unveils the important roles of bicarbonate: aiding the C-H activation and abstracting the β-proton in the second step of reductive elimination. The parallel bridging mode in the metal-olefin intermediate facilitates the syn-addition, explaining the experimentally observed stereoselectivity. The effect of the monodentate pyridine-based ligands is also discussed.

Fluorescent base analogues are of great importance as sensitive probes to detect the dynamic structures of DNA. In this research, the structural and photophysical properties of 13-mer oligonucleotides containing 4-aminophthalimide:2,4-diaminopyrimidine (4AP:DAP) (4AP0, 4AP') were characterized using both molecular dynamics simulations and quantum mechanics methods. The results indicate that the 4AP:DAP pair is well adapted to the overall B-DNA structure with higher stability and π-stacking abilities. The structural overlap of 4AP' and 4AP0 with the neighboring adenines only lies in the 5'-direction which results in the structure distortion from native B-DNA. Furthermore, the photophysical properties of the fluorescent base monomers and the B-DNA duplex were explored in detail. A very important result is that the hydrogen bond interaction does not have more effect on the fluorescence band apart from the slight red-shifts. In particular, the identity of the neighboring bases stacked with 4AP has an important effect on the fluorescence band. How the local environment can alter the photophysical features of the nucleobases when they are incorporated into the DNA duplex is elucidated.

Transition mental-catalyzed hydrothiolation of thiol and alkenes, alkynes or dienes is an important method to construct C-S bonds. To understand the control mechanism of the regioselectivity is of great significance in the hydrothiolation of 1,3-dienes which have two unsaturated C=C double bonds for a specific functionalization. In this paper, we explored the regioselective mechanisms of Rh(I)-catalyzed hydrothiolation of 1,3-dienes with different ligands by using density functional theory (DFT) and EDA analysis. The results reveal that the overall catalytic cycle consists of three elementary steps:(i) oxidant addition (ii) Rh-H insertion (iii) C-S reductive elimination. For the cationic catalysts Rh(cod)2SbF6 with JosiPhos ligand, the rate-determining step is Rh-H insertion, in whcih (S)-1,2-Markovnikov addition forming (S)-3a product, is most feasible among the six regio- and enantioselective pathways. The reasons for this phenomenon are steric repulsions and orbital interactions. While for electrically neutral catalysts the rate-determining step turns to be the C-S reductive elimination. The result uncovers that steric repulsions promots 3,4-anti-Markovnikov addition rather than that of 2,1-anti-Markovnikov.

Recently, a new synthetic methodology of rhodium-catalyzed carboamination/cyclopropanation from the same starting materials at different reaction conditions has been reported. It provides an efficient strategy for the stereospecific formation of both carbon- and nitrogen-based functionalities across an alkene. Herein we carried out a detailed theoretical mechanistic exploration for the reactions to elucidate the switch between carboamination and cyclopropanation as well as the origin of the chemoselectivity. Instead of the experimentally proposed RhIII–RhI–RhIII catalytic mechanism, our results reveal that the RhIII–RhV–RhIII mechanism is much more favorable in the two reactions. The chemoselectivity is attributed to a combination of electronic and steric effects in the reductive elimination step. The interactions between alkene and the rhodacycle during the alkene migration insertion control the stereoselectivity in the carboamination reactions. The present results disclose a dual role of the methanol so...

The Pd(ii)-catalyzed site-selective δ-C(sp3)-H alkenylation in the presence of more accessible γ-C(sp3)-H bonds is investigated by DFT calculations. Migratory insertion is found to be both the rate-limiting and the selectivity-determining step. The origin of the unusual site-selectivity is originally attributed to the different steric repulsion between the alkyne and palladacycle; however, our theoretical results reveal that the inherent electronic effect instead of steric repulsion determines the site-selectivity. The proposal is further validated by model calculations involving the less sterically hindered 1,2-dimethyl acetylene and acetylene. In addition, a novel HCO3--assisted N-H activation mechanism is reported, and the origin of the regioselectivity of an unsymmetrical alkyne is also studied.

Actinyl-tricarbonato anions [(AnO2)(CO3)3]4− (An = U–Cm) in various environments were investigated using theoretical approaches of quantum-mechanics, molecular-mechanics and cluster-models. Cations and solvent molecules in the 2nd coordination sphere affect the equatorial An←Oeq bonds more than the axial AnOax bonds. Common actinide contraction is found for calculated and experimental axial bond lengths of 92U to 94Pu, though no longer for 94Pu to 96Cm. The tendency of U to Pu forming actinyl(VI) species dwindles away toward Cm, which already features the preferred AnIII/LnIII oxidation state of the later actinides and all lanthanides. The well known change from d-type to typical U–Pu–Cm type and then to f-type behavior is labeled as the plutonium turn, a phenomenon that is caused by f-orbital energy-decrease and f-orbital localization with increase of both nuclear charge and oxidation state, and a non-linear variation of effective f-electron population across the actinide series. Both orbital and configuration mixing and occupation of antibonding 5f type orbitals increase, weakening the AnOax bonds and reducing the highest possible oxidation states of the later actinides.

Transition-metal-catalyzed carbonylation provides a useful approach to synthesize carbonyl-containing compounds and their derivatives. Controlling the regio-, chemo-, and stereoselectivity remains a significant challenge and is the key to the success of transformation. In the present study, we explored the mechanism and origins of the ligand-controlled regiodivergent carbonylation of alkynes with competitive nucleophilic amino and hydroxy groups by density functional theory (DFT) calculations. The proposed mechanism involves O(N)-cyclization, CO insertion, N-H(O-H) cleavage, C-N(C-O) reductive elimination and regeneration of the catalyst. The chemoselectivity is determined by cyclization. Instead of the originally proposed switch of competitive coordination sites, a new type of concerted deprotonation/cyclization model was proposed to rationalize the ligand-tuned chemoselectivity. The electron-deficient nitrogen-containing ligand promotes the flow of electrons during cyclization, and so it favors the O-cyclization/N-carbonylation pathway. However, sterically bulky and electron-rich phosphine controls the selectivity by a combination of electronic and steric effects. The improved mechanistic understanding will enable further design of selective transition-metal-catalyzed carbonylation.

A computational mechanistic study has been performed on Pd(II)-catalyzed enantioselective reactions involving acetyl-protected aminomethyl oxazolines (APAO) ligands that significantly improved reactivity and selectivity in C(sp

The origin of site selectivity of quinoline N-oxide substrate in Ir(III)-catalyzed amidation with tosyl azide was investigated computationally. The reaction proceeds exclusively at the C8 position, instead of the C2 position, which has been reported previously in many other reactions. C2-Amidation is kinetically impossible under the reaction condition according to our calculations, with high apparent activation energy up to 51.1 kcal/mol. The high energetic span is caused by the deep-lying 5-membered amido insertion intermediate, in which a strong stabilization effect was observed due to nN → π*C═N delocalization. For C8-amidation, however, the 6-membered counterpart is relatively unstable, making the activation energy only about half the value of C2-amidation. Meanwhile, denitrogenation is found to be turnover-limiting in the reaction. The oxidation state changes of the Ir center during the stepwise C–N bond formation were investigated, and a considerably higher effective oxidation state was found in the...

Density functional theory is utilized to elucidate the detailed mechanisms of the reactions between 2-aminooxazole O2/2-aminothiazole S2 and glyceraldehyde 2. According to our calculations, in O2/2 system, aminooxazoline O3 is formed via two steps including C C formation and cyclization. C C formation determines the reaction diastereoselectivity and ribo-aminooxazoline is the most favorable product. Although oxazole-hemiaminal O6 is not detected in the experiment, it is deduced can be formed theoretically. In S2/2 system, aminothiazoline S3 is hard to be generated because of the less nucleophilic ability of S2. The formation of thiazole-hemiaminal S6 is more favorable than S3 formation in kinetics but somewhat unfavorable in thermodynamics. However, the transformation from S6 to thiazole-aminal S7 is favorable both in kinetics and thermodynamics, which provides a driving force for the formation and transformation of S6. Additionally, our calculations indicate that phosphate is very important in assisting proton transfer in all of the transformations.

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.

A computational study of Cp*Co

Recycle of thorium is an essential process in the thorium-uranium closed fuel cycle of molten salt reactor (MSR). Pyrochemical treatment of spent nuclear fuel using chloride molten salts as medium has been considered as a promising method. In this article, we performed molecular dynamics simulations on the ThCl

The detailed mechanism of palladium-catalyzed γ-C(sp3)-H olefination/cyclization of triflyl-protected amines was investigated by density functional theory (DFT) calculations. The olefinated intermediate was initially formed in the first catalytic cycle involving ligand exchange, bicarbonate-assisted C(sp3)-H bond cleavage, alkene insertion and 'reductive β-hydride elimination'. The following syn-addition and reductive elimination furnish the aza-Wacker product. The first step of reductive elimination is the rate-determining step. The mechanism unveils the important roles of bicarbonate: aiding the C-H activation and abstracting the β-proton in the second step of reductive elimination. The parallel bridging mode in the metal-olefin intermediate facilitates the syn-addition, explaining the experimentally observed stereoselectivity. The effect of the monodentate pyridine-based ligands is also discussed.

A Rh

The reaction mechanism and the origins of regio- and enantioselectivities for Pd-catalyzed asymmetric arylation of aliphatic α-amino anion equivalents were investigated computationally. The results indicate that the reaction proceeds via mainly six sequential steps: deprotonation at α'-site of imine, coordination of α-amino anion to Pd-catalyst, oxidative addition, transmetalation, reductive elimination, as well as the final dissociation to release the product and regenerate the catalyst. The transmetalation is a key step on which both enantioselectivity and regioselectivity depend. The charge inversions of α- and α'-C atoms and the orbital interaction between Pd center and α-C in transmetalation step are responsible for the regioselectivity. Additionally, the intermediates before the dissociation step are critical in controlling the enantioselectivity. Noncovalent interactions analyses indicate that the enantioselectivity primarily arises from the CH···π interactions of isopropyl (iPr) groups with the fluorene and the benzene rings for PdL

Computational studies have been applied to gain insight into the mechanism of Pd(II) catalyzed α-C–H functionalization of N-methoxy cinnamamide. The results show that the whole catalytic cycle proceeds via sequential six steps, including (i) catalyst Pd(t-BuNC)2 oxidation with O2, (ii) O–H deprotonation, (iii) t-BuNC migratory insertion to the Pd–C bond, (iv) acyl migration, (v) C–H activation and (vi) reductive elimination. The regioselectivity for different C–H activation sites depends on the coordination structures of α-C or β-C to the palladium(II) center. The coordination of α-C to the palladium(II) center shows a regular planar quadrilateral structure, which is stable. However, the β-C coordinating to the palladium(II) center mainly exhibits a distorted quadrilateral structure, which is relatively unstable. Thus, the barrier of α-C–H activation is much lower than that of β-C–H activation. The present results provide a deep understanding of the site-selectivity of C–H activation.

Actinyl-tricarbonato anions [(AnO

LiF-ThF4 molten salt (MS) is the fuel for advanced MS reactors. Knowledge of the microscopic MS structure and dynamics is required for an understanding of the macroscopic physical and chemical properties of the MS phases. We have performed molecular dynamics simulations on LiF-ThF4 MS at different molar percentages (LiF/ThF4 = 20.0 to 0.5) and temperatures (1100 to 1400 K). Experimental deductions and recent theoretical results on the coordination structures and transport properties of the MS are well reproduced. The density of states of the [ThF8](4-) species and the character of the Th-F bonding are investigated. The interplay between the microscopic structures and the dynamical properties is elucidated. Corresponding to the smaller effective radius of Zr, the activation barrier of the M(4+)-F(-) dissociation and the lifetime of the first coordination shell of M(4+) are both smaller for M = Th than for M = Zr in the respective LiF-MF4 systems. The shorter Zr-F bond is stronger than the longer Th-F bond, while the coordination number of the predominant [ZrF7](3-) species is smaller than that of the dominant [ThF8](4-) species. An approximate formula is proposed for the lifetime of F(-) ions in the first solvation shell of molten MFn (M = Y, Zr, Th) in terms of the radial distribution function.

The mechanism of redox-neutral Rh(III)-catalyzed coupling reactions of arylnitrones with alkynes was investigated by density functional theory (DFT) calculations. The free energy profiles associated with the catalytic cycle, involving C(sp2)–H activation, insertion of alkyne, transfer of O atom, cyclization and protodemetalation, are presented and analyzed. An overwhelming preference for alkyne insertion into Rh–C over Rh–O is observed among all pathways, and the most favorable route is determined. The pivalate-assisted C–H activation step is turnover-limiting, and the cyclization step determines the diastereoselectivity of the reaction, with the stereoselectivity arising mainly from the difference of noncovalent interactions in key transition states. The detailed mechanism of O atom transfer, RhIII–RhI–RhIII versus RhIII–RhV–RhIII cycle, is discussed.

Theoretical calculation has been carried out for the nucleophilic displacement reaction of 1,2-dichloroethane catalyzed by haloalkane dehalogenase. The results indicate that different hydrogen bond patterns of the oxyanion hole and the halide-stabilizing residues play an important role in the dehalogenation reaction. They cause concertedly an earlier transition state (TS) with the activation barrier of 16.60 kcal/mol. The stabilization effect of Trp125 and Trp175 on chlorine atom in the TS is larger than that of the reactant complex by 15.67 kcal/mol so that, they make contribution to the stabilization of the TS. Moreover, the reaction shows the enzymatic action can be attributed to a combination of reactant-state destabilization and transition-state electrostatic stabilization. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

The decomposition of triphenyl phosphite ozonide (TPPO) has been well recognized as a potential source of singlet oxygen (O2, 1Δg) for the chemical oxygen–iodine laser. Experimental observations suggested that ammonia or pyridine water solution can accelerate the decomposition of TPPO, and hydroxyl ion is responsible for accelerating singlet oxygen liberation during this decomposition. In this paper, we studied the mechanism of OH−-accelerated reaction using density functional theory (DFT) at B3LYP/6-31+G* levels of theory. The calculations reveal a favorable free energy pathway for hydroxide-accelerated decomposition of TPPO, i.e. nucleophilic addition at phosphorus, followed by elimination of phenoxy group and subsequent liberation of singlet oxygen. The solvent effects were studied using a polarizable continuum model. The frontier molecular orbitals of the ozonides, atom–atom Wiberg bond index and corresponding atomic charges were also investigated to shed further light on the reaction pathway.

We report a practical approach, the first of its kind, to construct nanoscale UiO-type metal-organic framework (Mi-UiO-66 and Mi-UiO-67) fluorescent probes for the detection of Cys and GSH. They showed high sensitivity (10(-11) M) and selectivity for Cys and GSH, and their fluorescence imaging of Cys and GSH in living cells was well demonstrated.

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.

Experimentally and theoretically derived interatomic distances (D) and ionic radii (R) of more than a hundred monomeric (AX), dimeric (A2X2, ABXY), and crystalline ([AX]) alkali halide species (A=Li, Na, K, Rb, Cs, Fr; X=H, F, Cl, Br, I, At) have been analyzed. Chemists use the word "atomic radius" for two antithetic concepts. Let D(CiEE'jj') be the "billion" of distances i between two adjacent atoms in the millions of known compounds C from a hundred different elements E in bonding states j. The common chemical aim is partitioning D approximately into increments R(Ej) +R(E'j'). This can be achieved with a few (say

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.