Zwitterionic Transition State Research Articles

Competition between [2\u2009+\u20091]- and [4\u2009+\u20091]-cycloaddition mechanisms in reactions of conjugated nitroalkenes with dichlorocarbene in the light of a DFT computational study

The competition between [2 + 1] and [4 + 1] channels regarding reactions of conjugated nitroalkenes with dichlorocarbene was explored based on B3LYP/6-31G(d) calculations. It was found that, in the case of cycloadditions involving parent nitroethene and its 1-substituted analogs, the [2 + 1] scheme should be treated as possible only from the kinetic process point of view. On the other hand, in similar reactions involving 2-substituted nitroethenes, both channels considered may compete. Additionally, mechanistic aspects of all cycloadditions were analyzed. It was found that the considered [2 + 1]-cycloadditions proceed via a non-polar mechanism with a biradicaloidal transition state (TS), whereas [4 + 1]-cycloadditions proceed via a polar mechanism with a zwitterionic TS.

Water enables an asymmetric cross reaction of α-keto acids with α-keto esters for the synthesis of quaternary isotetronic acids.

A water promoted asymmetric aldol/lactonization/enolization cascade reaction of α-keto acids and α-keto esters was developed, affording the first general protocol for the construction of chiral quaternary isotetronic acids with excellent enantioselectivity. Theoretical results indicate that intramolecular ionized enamine intermediates stabilized by water generate zwitterionic transition states in a lower activation energy and higher face selectivity, resulting in high activity and chemo- and enantioselectivity.

Stepwise versus Concerted Reductive Elimination Mechanisms in the Carbon–Iodide Bond Formation of (DPEphos)RhMeI2 Complex

Reductive elimination is the key bond formation process of organometallic reactions. Goldberg and co-workers recently revealed an unprecedented competition of parallel stepwise reductive elimination pathways for the carbon–iodide bond formation of (DPEphos)RhMeI2 complex. To understand the controlling factors that differentiate the concerted and stepwise pathways, we performed density functional theory (DFT) calculations to elucidate the mechanistic details. The competing stepwise pathways were identified as the anionic and zwitterionic stepwise pathways. The anionic pathway involves the direct SN2 attack of the external iodide anion to the methyl group, leading to the observed carbon–iodide bond formation. Alternatively, heterolytic Rh–I bond cleavage generates the cationic (DPEphos)RhMeI+ intermediate, and the subsequent SN2 attack of the iodide anion to the methyl group occurs via the zwitterionic transition state. In comparison with the stepwise reductive elimination pathways, the classic concerted pa...

DFT Studies on the Reactions of Boroles with Alkynes.

DFT calculations were performed to investigate the reactions of boroles with alkynes, in which boranorbornadiene, borepin and/or boracyclohexadiene can be formed depending on the substituents on the borole and alkyne. Our computational results indicated that formation of boranorbornadiene and borepin is generally kinetically favoured and that the products can interconvert. Formation of boracyclohexadiene is kinetically unfavourable in most reactions. However, certain substituents can promote the formation of boracyclohexadiene by stabilizing an energetically high-lying zwitterionic transition state that leads to boracyclohexadiene. Borafluorene reacted with most alkynes to give borepin exclusively due to its propensity to maintain its aromaticity. However, when it reacted with silyl-substituted alkyne(s), a novel product, different from boranorbornadiene, borepin and boracyclohexadiene was generated, which can be attributed to the well-known ability of silyl groups to migrate.

When To Let Go-Diradical Intermediates from Zwitterionic Transition State Structures?

Several Brummond-Chen thermal intramolecular (2 + 2)-cycloaddition reactions were examined using density functional theory calculations. The results of these calculations indicate that it is possible for these reactions to involve diradical intermediates that form directly from zwitterionic transition state structures. The likelihood of this scenario was shown to be sensitive to both the nature of substituents and solvent polarity.

Reactivity of an N‐Heterocyclic Carbene Stabilized Hydrosilylene towards a Ketone and CO2: Experimental and Theoretical Study

The reaction of N‐heterocyclic carbene (NHC)‐stabilized hydrosilylene 1, tBu3SiSi(H)←NHC, with one and two equivalents of benzophenone gave rise to bicyclic compounds 2 and 3, tBu3Si(R)[Si‐CH2‐N(CMeCMeNMe)‐CPh2‐O] (R = H, OCHPh2). The NHC plays a crucial role in this reactivity, as it is directly involved in C–C bond formation and supplies the C–H‐activated methyl group. In the formation of 3, the terminal Si–H bond of the hydrosilylene is involved in transition‐metal‐free hydrosilylation. All steps in these mechanisms are based on NHC‐stabilized zwitterionic transition states and intermediates and were investigated by utilizing DFT calculations. In addition, the CO2 activation of 1 to yield cis/trans‐cyclotrisiloxane 4, [(tBu3Si)(H)Si‐O]3, stereoselectively and its mechanistic study are reported.

How many tautomerization pathways connect Watson–Crick-like G*·T DNA base mispair and wobble mismatches?

In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson–Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pathway is eligible from a biological perspective. It involves short-lived intermediate – the G·T*(WC) base mispair – and is governed by the planar, highly stable, and zwitterionic transition state stabilized by the participation of the unique pattern of the five intermolecular O6+H⋯O4−, O6+H⋯N3−, N1+H⋯N3−, N1+H⋯O2−, and N2+H⋯O2− H-bonds. This non-dissociative G·T(w) ↔ G*·T(WC) tautomerization occurs without opening of the pair: Bases within mispair remain connected by 14 different patterns of the specific intermolecular interactions that successively change each other along the IRC. Novel kinetically controlled mechanism of the thermodynamically non-equilibrium spontaneous point GT/TG incorporation errors has been suggested. The mutagenic effect of the analogues of the nucleotide bases, in particular 5-bromouracil, can be attributed to the decreasing of the barrier of the acquisition by the wobble pair containing these compounds of the enzymatically competent Watson–Crick’s geometry via the intrapair mutagenic tautomerization directly in the essentially hydrophobic recognition pocket of the replication DNA-polymerase machinery. Proposed approaches are able to explain experimental data, namely growth of the rate of the spontaneous point incorporation errors during DNA biosynthesis with increasing temperature.

Push-Pull Buta-1,2,3-trienes: exceptionally low rotational barriers of cumulenic C=C bonds and proacetylenic reactivity.

A variety of asymmetrically donor-acceptor-substituted [3]cumulenes (buta-1,2,3-trienes) were synthesized by developed procedures. The activation barriers to rotation ΔG(≠) were measured by variable temperature NMR spectroscopy and found to be as low as 11.8 kcal mol(-1) , in the range of the barriers for rotation around sterically hindered single bonds. The central C=C bond of the push-pull-substituted [3]cumulene moiety is shortened down to 1.22 Å as measured by X-ray crystallography, leading to a substantial bond length alternation (BLA) of up to 0.17 Å. All the experimental results are supported by DFT calculations. Zwitterionic transition states (TS) of bond rotation confirm the postulated proacetylenic character of donor-acceptor [3]cumulenes. Additional support for the proacetylenic character of these chromophores is provided by their reaction with tetracyanoethene (TCNE) in a cycloaddition-retroelectrocyclization (CA-RE) cascade characteristic of donor-polarized acetylenes.

Evidence for a zwitterionic transition state in double bond rotations within tungsten-vinyl complexes.

The trianionic pincer supported tungsten-vinyl complex [CF3-ONO]W(O){(CH3)3CC[double bond, length as m-dash]C(CH3)2} (3syn) undergoes facile double bond rotation at ambient temperature. The degenerate methyl exchange rates were measured via selective inversion-recovery experiments. DFT computations in conjunction with experimentally determined rate constants support a double bond rotation that proceeds via a Zwiterionic transition state.

Reaction of an N-heterocyclic carbene-stabilized silicon(II) monohydride with alkynes: [2+2+1] cycloaddition versus hydrogen abstraction.

An in depth study of the reactivity of an N-heterocyclic carbene (NHC)-stabilized silylene monohydride with alkynes is reported. The reaction of silylene monohydride 1, tBu3 Si(H)Si←NHC, with diphenylacetylene afforded silole 2, tBu3 Si(H)Si(C4 Ph4 ). The density functional theory (DFT) calculations for the reaction mechanism of the [2+2+1] cycloaddition revealed that the NHC played a major part stabilizing zwitterionic transition states and intermediates to assist the cyclization pathway. A significantly different outcome was observed, when silylene monohydride 1 was treated with phenylacetylene, which gave rise to supersilyl substituted 1-alkenyl-1-alkynylsilane 3, tBu3 Si(H)Si(CHCHPh)(CCPh). Mechanistic investigations using an isotope labelling technique and DFT calculations suggest that this reaction occurs through a similar zwitterionic intermediate and subsequent hydrogen abstraction from a second molecule of phenylacetylene.

Quantum Mechanical Study on the Mechanism of Peptide Release in the Ribosome

A quantum mechanical study of different concerted mechanisms of peptide release in the ribosome has been carried out using the M06-2X density functional. Reoptimization with MP2 has also been carried out for the stationary points of some selected mechanisms. The uncatalyzed processes in solution have been treated with the SMD solvation model. We conclude that the 2'-OH plays an important catalytic role and that it takes place via a zwitterionic transition state, this TS being stabilized by the presence of oxyanion holes or by the solvent. The comparison with our previous study on the peptide bond formation shows that both processes proceed via two different mechanisms, in such a way that the TS of the aminolysis has an ion-pair instead of a zwitterionic character. So, despite the limitations of the model we have used, we can conclude that there is catalytic promiscuity at the peptidyl transferase center (PTC) of the ribosome.

Rearrangements of Acyl, Thioacyl, and Imidoyl (Thio)cyanates to Iso(thio)cyanates, Acyl Iso(thio)cyanates to (Thio)acyl Isocyanates, and Imidoyl Iso(thio)cyanates to (Thio)acyl Carbodiimides, RCX-YCN ⇌ RCX-NCY ⇌ RCY-NCX ⇌ RCY-XCN (X and Y = O, S, NR′)

Two types of rearrangements have been investigated computationally at the B3LYP/6-311+G(d,p) level. The activation barriers for rearrangement of acyl thiocyanates RCO-SCN to the corresponding isothiocyanates RCO-NCS are 30-31 kcal/mol in agreement with the observation that the thiocyanates are in some cases isolable albeit very sensitive compounds. Alkoxycarbonyl-, (alkylthio)carbonyl- and carbamoyl thiocyanates are isolable and have higher calculated barriers (ca. 40 kcal/mol) toward rearrangement to isothiocyanates, whereas all thioacyl thiocyanate derivatives are rather unstable compounds with barriers in the range 20-30 kcal/mol for rearrangement to the isothiocyanates. Acyl-, alkoxycarbonyl-, and carbamoyl cyanates R-CO-OCN are predicted to be in some cases isolable compounds with barriers up to ca. 40 kcal/mol for rearrangement to the isocyanates RCO-NCO. All of the rearrangements of this type involve the HOMO of a nearly linear (thio)cyanate anion and the LUMO of the acyl cation, in particular the acyl C═X π* orbital. The second type of rearrangement involves 1,3-shifts of the groups R attached to the (thio)acyl groups, that is, acyl isothiocyanate-thioacyl isocyanate and imidoyl isothiocyanate-thioacyl carbodiimide rearrangements. These reactions involve four-membered cyclic, zwitterionic transition states facilitated by lone pair-LUMO interactions between the migrating R group and the neighboring iso(thio)cyanate function. Combination of the two rearrangements leads to the general reaction scheme RCX-YCN ⇌ RCX-NCY ⇌ RCY-NCX ⇌ RCY-XCN (X and Y = O, S, NR').

Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: an exhaustive quantum-chemical analysis

The molecular structures, relative stability order, and dipole moments of a complete family of 21 planar hypoxanthine (Hyp) prototropic molecular–zwitterionic tautomers including ylidic forms were computationally investigated at the MP2/6–311++G(2df,pd)//B3LYP/6–311++G(d,p) level of theory in vacuum and in three different surrounding environments: continuum with a low dielectric constant (ϵ = 4) corresponding to a hydrophobic interface of protein–nucleic acid interactions, dimethylsulfoxide (DMSO), and water. The keto-N1HN7H tautomer was established to be the global minimum in vacuum and in continuum with ϵ = 4, while Hyp molecule exists as a mixture of the keto-N1HN9H and keto-N1HN7H tautomers in approximately equal amounts in DMSO and in water at T = 298.15 K. We found out that neither intramolecular tautomerization by single proton transfer in the Hyp base, nor intermolecular tautomerization by double proton transfer in the most energetically favorable Hyp·Hyp homodimer (symmetry C 2h ), stabilized by two equivalent N1H…O6 H-bonds, induces the formation of the enol tautomer (marked with an asterisk) of Hyp with cis-oriented O6H hydroxyl group relative to neighboring N1C6 bond. We first discovered a new scenario of the keto–enol tautomerization of Hyp · Hyp homodimer (C 2h ) via zwitterionic near-orthogonal transition state (TS), stabilized by N1+H…N1− and O6+H…N1− H-bonds, to heterodimer Hyp∗ · Hyp (C s ), stabilized by O6H…O6 and N1H…N1 H-bonds. We first showed that Hyp∗ · Thy mispair (C s ), stabilized by O6H…O4, N3H…N1, and C2H…O2 H-bonds, mimicking Watson–Crick base pairing, converts to the wobble Hyp · Thy base pair (C s ), stabilized by N3H…O6 and N1H…O2 H-bonds, via high- and low-energy TSs and intermediate Hyp · Thy∗, stabilized by O4H…O6, N1H…N3, and C2H…O2 H-bonds. The most energetically favorable TS is the zwitterionic pair Hyp+ · Thy− (C s ), stabilized by O6+H…O4−, O6+H…N3−, N1+H…N3−, and N1+H…O2− H-bonds. The authors expressed and substantiated the hypothesis, that the keto tautomer of Hyp is a mutagenic compound, while enol tautomer Hyp∗ does not possess mutagenic properties. The lifetime of the nonmutagenic tautomer Hyp∗ exceeds by many orders the time needed to complete a round of DNA replication in the cell. For the first time purine–purine planar H-bonded mispairs containing Hyp in the anti-orientation with respect to the sugar moiety – Hyp · Ade syn , Hyp · Gua∗ syn , and Hyp · Gua syn , that closely resembles the geometry of the Watson–Crick base pairs, have been suggested as the source of transversions. An influence of the surrounding environment (ϵ = 4) on the stability of studied complexes and corresponding TSs was estimated by means of the conductor-like polarizable continuum model. Electron-topological, structural, vibrational, and energetic characterictics of all conventional and nonconventional H-bonds in the investigated structures are presented. Presented data are key to understanding elementary molecular mechanisms of mutagenic action of Hyp as a product of the adenine deamination in DNA.

Investigation of the Origins of Regiochemical Control in [4+2] Cycloadditions of 2-Pyrones and Alkynylboronates

The [4+2] cycloaddition of 2-pyrones with substituted alkynylboronates has been studied. In general, the highest yielding cycloadditions were obtained in reactions that employed a trimethylsilyl-substituted alkynylboronate. The highest regioselectivities were obtained using the corresponding phenyl-substituted alkyne, which provided a single regioisomer irrespective of the 2-pyrone used. Mechanistic studies suggest that the high regioselectivity observed is due to stabilization of a zwitterionic transition state.

Theoretical Study on Hetero‐Diels–Alder Reaction of Butadiene with Benzaldehyde Catalyzed by Chiral InIII Complexes

AbstractThe mechanism of the hetero‐Diels–Alder reaction of butadiene with benzaldehyde catalyzed by chiral N,N′‐dioxide/In(OTf)3 complexes was studied theoretically by using density functional theory (DFT) and model system. The computational results indicate that the catalyzed reaction proceeded through a concerted mechanism via a highly zwitterionic transition state. The lowest energy barrier was 11.8 kJ mol–1, which is 63.0 kJ mol–1 lower than that of the uncatalyzed reaction. The results indicate that the endo approach is advantageous over the exo approach, because exo transitions states suffer from more steric hindrance than the endo transitions states as a result of interactions among the substrates, the trifluoromethanesulfonic group and the R4 groups of the ligand. The (S) configuration was observed predominantly over the (R) form, because there is no distinguishable repulsion between butadiene and the exo amino side or the endo amino side of the ligand. Besides, the interactions between the terminal hydrogen atoms of butadiene and the oxygen atoms of the trifluoromethanesulfonic group make the structure more stable. Thus, the experimental results were explained well by calculation of the chiral N,N′‐dioxide/In(OTf)3 complex catalyzed hetero‐Diels–Alder reaction at the molecular level.

Water as dual functional cocatalyst: A theoretical study on the mechanism of direct aldol reaction on water catalyzed by a leucine derivative

The role of water and stereoselectivity in the direct syn-aldol reaction involving 3-pentanone and 4-nitrobenzaldehyde catalyzed by amino acid derivatives on water has been investigated by density functional theory. Calculations indicate that the formation of intermediate enamine is the rate determining step via a three-step process with activation enthalpies of 50 kcal/mol in the gas phase and 21 kcal/mol in the presence of water. The subsequent nucleophilic addition of enamine to aldehyde is relatively easier with activation enthalpies below 10 kcal/mol both in the gas phase and in the presence of water. The diastereoselective formation of syn- and anti-aldol products results from the preferential formation of Z-enamine to E-enamine, kinetically and thermodynamically. The enantioselectivity of both syn- and anti-products is controlled by the steric repulsive interactions between the amino alcohol moiety of catalyst and the phenyl ring of aldehyde. Calculations show that water molecule can act as a proton shuttle in the proton-transport catalytic processes. The water-assisted proton-transfer is very efficient to reduce the activation barriers via protonation and deprotonation in the formation of C-N and C-C bonds, dehydration, and β-elimination processes by inhibiting the generation of zwitterionic transition states. The theoretical discoveries indicate that in the present proton-transport assistance, the amino alcohol moiety of the catalyst plays a critical role as hydrogen bond donor to anchor substrates with carbonyl group close to the amine or enamine moiety so that the water molecule can bridge the NH of amine and the oxygen of carbonyl by hydrogen bonding interaction around the reactive site to activate the reactants and promote the reaction effectively.

Hydration of acetone in the gas phase and in water solvent

In water solvent, the hydration of acetone proceeds by a cyclic (cooperative) process in which concurrent C–O bond formation and proton transfer to oxygen take place through a solvent and (or) catalyst bridge. Reactivity is determined primarily by the concentration of a reactant complex and not the barrier from this complex. This situation is reversed in the gas phase; although the concentrations of reactive complexes are much higher than in solution, the barriers are also higher and dominant in determining reactivity. Calculations of isotope effects suggest that multiple hydron transfers are synchronous in the gas phase to avoid zwitterionic transition states. In solution, such transition states are stabilized by solvation and hydron transfers can be asynchronous.

DFT Study on Bifunctional Chiral Brønsted Acid-Catalyzed Asymmetric Hydrophosphonylation of Imines

Asymmetric hydrophosphonylation reaction of aldimines with dialkyl phosphites proceeds catalytically by means of a phosphoric acid diester, derived from (R)-BINOL, as a chiral Brønsted acid to afford alpha-amino phosphonates with good to high enantioselectivities (up to 90% ee). The use of the aldimines derived from cinnamaldehyde derivatives and sterically demanding dialkyl phosphites was essential for achieving high enantioselectivity as well as high yield. To elucidate the reaction mechanism and the origin of the high enantioselectivity, DFT calculation (BHandHLYP/6-31G*) was carried out. The reaction proceeds via the nine-membered zwitterionic transition state (TS) with the chiral phosphoric acid, where aldimine and phosphite could be activated by the Brønsted acidic site and Lewis basic site, respectively. The si-facial attacking TS could be less favored by the steric repulsion of 3,3'-aryl groups on the chiral phosphoric acid with the bulky phosphite. When using the aldimine derived from benzaldehyde, the re-facial attacking TS is destabilized to decrease the enantioselectivity in agreement with the experimental results.

Rearrangement of 1,3-Dipolar Cycloadducts Derived from Bis(phenylazo)stilbene: A DFT Level Mechanistic Investigation

The 1,3-dipolar cycloaddition of bis(phenylazo)stilbene with activated ethene and ethyne derivatives and the subsequent rearrangement of the cycloadducts have been studied using model compounds at the B3LYP/6-31G(d) level of density functional theory (DFT). From the structural and electronic features, a five-membered zwitterionic ring system 9 (1,2,3-triazolium-1-imide system) formed from bis(phenylazo)ethylene is confirmed as the active 1,3-dipole species in the reaction. Formation of the 1,3-dipolar cycloadduct from the alkyne derivative is found to be 26.0 kcal/mol exergonic, and it requires an activation free energy of 19.4 kcal/mol. The 1,3-cycloadduct formed in the reaction undergoes a very facile migration of a nitrogen-bearing fragment, passing through a zwitterionic transition state. A small activation free energy of 8.2 kcal/mol is observed for this step of the reaction, and it is 19.6 kcal/mol exergonic. Further activation of the newly formed rearranged product is possible under elevated temperatures, again passing through a zwitterionic transition state and resulting in the formation of 2,5-dihydro-1,2,3-triazine derivatives. Such derivatives have been recently reported by Butler et al. (J. Org. Chem. 2006, 71, 5679). The charge separation in 9 and the zwitterionic transition states are stabilized through the pi-system of the phenyl rings and the carbonyl groups. Similar structural, electronic, and mechanistic features are obtained for the reaction of 9 with the ethylenic dipolarophile acrylonitrile. Molecular electrostatic potential analyses of the 1,3-dipole and the zwitterionic transitions states are found to be very useful for characterizing their electron delocalization features. The solvation effects can enhance the feasibility of these reactions as they stabilize the zwitterionic transition states to a great extent.

Photosensitized Oxidation of Oxopurines by Rose Bengal†

AbstractPhotosensitized oxidations of oxopurines (OP) as caffeine, theophylline, theobromine and 1,3,7‐trimethyluric acid (TMU) by Rose Bengal were investigated. In all cases photooxidations occur by a type II mechanism. Reactive and nonreactive 1O2 quenching rate constants by OP were determined in different solvents. Based on the correlations of the rate constants with different solvent parameters (α, β, ET[30], AN, DN, *,), the initial formation of an exciplex between 1O2 and OP is proposed that evolves to a zwitterionic transition state. Some reaction products were characterized, among them 3‐mefh‐yl‐5‐(methylamine)‐1,5‐dehydrohydantoin was obtained as the main photooxidation product of TMU. A reaction mechanism is proposed for the formation of this and other reaction products.