A general equation correlating intramolecular rates with ‘attack’ parameters: distance and angle

Using density functional theory (DFT) at the B3LYP level with the 6-31G(d,p) basis set, a general equation is derived relating activation energy with the distance between the two reactive centers (r_GM), and the hydrogen-bonding angle (α_GM) in an intramolecular proton transfer process. The strong correlation between the values of r_GM and α_GM with the activation energy, ΔG^‡, which reflects the experimental reaction rate, provides an excellent tool to predict reaction rate based on calculated geometrical parameters for a certain system (ΔH^‡, ΔG^‡ vs r_GM and α_GM). The slope of the equation can be used as an indicator of the mode by which the two reacting centers orchestrate in an intramolecular process.     

The efficiency of proton transfer in Kirby’s enzyme model, a computational approach

DFT and ab initio calculation results for proton transfer reactions in Kirby’s acetals reveal that the mechanism proceeds via efficient intramolecular general acid catalysis (IGAC) and not through a ‘classical’ general acid catalysis mechanism (GAC). Further, they show that the driving force for the proton transfer efficiency is the proximity of the two reactive centers (r) and the attack angle (α), and the rate of the reaction is linearly correlated with r² and sin (180° − α). Acetals with short r values and with α values close to 180° (forming a linear H-bond) are more reactive due to the development of strong hydrogen bonds in their global minimum, transition state, and product structures.     

Molecular structure of NiO<Subscript>2</Subscript>N<Subscript>2</Subscript>C<Subscript>16</Subscript>H<Subscript>14</Subscript> from gas-phase electron diffraction and quantum chemical data

Gas-phase electron diffractometry was used to study the molecular structure of N,N′-ethylenebis(salicylaldiminato)nickel(II), NiO₂N₂C₁₆H₁₄, [hereinafter Ni(salen)] at 583(5) K. The molecule has C ₂ symmetry with a practically planar structure of the NiN₂O₂ coordination unit and with internuclear distances r _α (Ni-O) = 1.882(21) Å and r _α (Ni-N) = 1.889(22) Å. The results of B3LYP/CEP-31G molecular structure calculations are in good agreement with experimental data, whereas the RHF/CEP-31G method significantly overestimates the Ni-N internuclear distance and gives worse results for other structural parameters. According to 3LYP/CEP-31G calculations, the ¹ A low-spin state is 28 kJ/mole lower in energy than the ³ B high-spin state.     

Palladium-catalyzed stereoselective intramolecular cyclization and Suzuki coupling of N-arylsulfonyl-α-chloroenamides promoted by a γ-hydroxy group

The Suzuki reaction of both (E)- and (Z)-α-chloro-γ-hydroxyenamides with benzeneboronic acid by using Pd₂(dba)₃, tBu₃P, and Cs₂CO₃ proceeded stereoselectively to afford only (E)-trisubstituted enamides. Also, palladium-catalyzed intramolecular cyclization of (E)- and (Z)-α-chloro-γ-hydroxyenamides bearing an N-arylsulfonyl group took place stereoselectively to give the corresponding (E)-2,3-dihydrobenzoisothiazole 1,1-dioxides. The γ-hyroxy group in α-chloroenamides was found to accelerate the present palladium-catalyzed carbon-carbon bond forming reactions.     

A theoretical approach to the formation mechanism of diphenyldithieno[3,2-b:2′,3′-d]thiophene from 1,8-diketone, 4,5-bis(benzoylmethylthio)thiophene: a DFT study

The mechanism of formation of dithieno[3,2-b:2′,3′-d]thiophene (DTT) through the reaction of 1,8-diketone, 4,5-bis(benzoylmethylthio)thiophene with P₄S₁₀ was examined in detail by employing DFT method at B3LYP/6-311+G(d,p) level. Two mechanisms were considered. The first one included two parts (i) transformation of the 1,8-diketone, 4,5-bis(benzoylmethylthio)thiophene to the dithione by the reaction of P₄S₁₀ with the carbonyl groups and (ii) cyclization of the dithione to the final product, DTT, through an intramolecular reaction of the thiophene with thiones. The second mechanism consists of an initial attack of the carbonyl oxygen to the phosphorus atom of P₄S₁₀ followed by cyclization via an intramolecular attack from the thiophene ring to the highly electrophilic carbons connected to the oxygens to form DTT. According to the calculated Gibbs free energies of the studied paths, the second mechanism is more favorable than the first one and both pathways proceed in a stepwise manner.     

A novel route to 2-imidazolin-5-one derivatives via oxidative cyclization of aryl-substituted (Z)-N-acetyl-α-dehydroalanines having a dialkylamino group

It was found that the reaction of the title compounds [(Z)-1] with oxygen in methanol proceeds according to the first-order kinetics to give (Z)-2-imidazolin-5-one derivatives and hydrogen peroxide in quantitative yields. Analysis of substituent and solvent effects on the rate constant for this oxidative cyclization led us to propose that electron transfer from the dialkylamino nitrogen in (Z)-1 to oxygen, amide-proton abstraction by superoxide and the subsequent intramolecular electron transfer are all rate-determining steps. The synthetic utility of the novel cyclization reaction of aryl-substituted (Z)-N-acetyl-α-dehydroalanine derivatives was discussed.     

Inequivalence of substitution pairs in hydroxynaphthaldehyde: A theoretical measurement by intramolecular hydrogen bond strength,aromaticity, and excited‐state intramolecular proton transfer reaction

The inequivalence of substitution pair positions of naphthalene ring has been investigated by a theoretical measurement of hydrogen bond strength, aromaticity, and excited state intramolecular proton transfer (ESIPT) reaction as the tools in three substituted naphthalene compounds viz 1‐hydroxy‐2‐naphthaldehyde (HN12), 2‐hydroxy‐1‐naphthaldehyde (HN21), and 2‐hydroxy‐3‐naphthaldehyde (HN23). The difference in intramolecular hydrogen bond (IMHB) strength clearly reflects the inequivalence of substitution pairs where the calculated IMHB strength is found to be greater for HN12 and HN21 than HN23. The H‐bonding interactions have been explored by calculation of electron density ρ(r) and Laplacian ?²ρ(r) at the bond critical point using atoms in molecule method and by calculation of interaction between σ* of OH with lone pair of carbonyl oxygen atom using NBO analysis. The ground and excited state potential energy surfaces (PESs) for the proton transfer reaction at HF (6‐31G**) and DFT (B3LYP/6‐31G**) levels are similar for HN12, HN21 and different for HN23. The computed aromaticity of the two rings of naphthalene moiety at B3LYP/6‐31G** method also predicts similarity between HN12 and HN21, but different for HN23. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Analyzing the efficiency of proton transfer to carbon in Kirby’s enzyme model—a computational approach

A mechanistic study using ab initio and DFT calculation methods on the intramolecular ring-closing of enol ethers 1Z, 1E, and 2 (Kirby’s enzyme models for aldolase and isomerase) has revealed that proton transfer is the rate determining step and involves two stages: re-organization of the global minimum structure (having the lowest enthalpic energy and a relatively long distance between the two reactive centers, r) to a more organized ground state conformation (having the smallest r distance among all the conformations), and a second stage by which the proton is transferred from the organized state to the corresponding transition state. The energy needed for the first stage to occur is dependent on the rotation barrier for the proton to be in proximity to the CC double bond carbon (proximity effects), whereas, that needed for the second step is largely affected by the strain energies of the reactant and the corresponding product. In addition, it was found that the oxocarbocation intermediate involved in the proton transfer is unstable and undergoes ring-closing to the corresponding product with zero activation energy. Further, the calculated DFT effective molarities (EM) for 1Z, 1E, and 2 were found to correlate strongly with experimental EM values.     

Synthetic investigations of (1,3′)-bistetrahydroisoquinolines: towards pentacyclic analogues of piperazine core alkaloids

Synthetic investigations of (1,3′)-bistetrahydroisoquinolines are reported as the key intermediates for the synthesis of ecteinascidin and phthalascidin pentacyclic structure analogues through successive Pictet-Spengler cyclization and intramolecular peptide coupling. The direct Pictet-Spengler reaction between a derivative of l-DOPA and N-protected-α-aminoaldehyde was first extended to the synthesis of cis-(1,3′)-bistetrahydroisoquinoline. After introduction of the required amino acid moiety, an efficient six-membered ring intramolecular peptide coupling gave rise to piperazine derivative structures. Complete structural assignments were corroborated by NMR and X-ray spectroscopic methods. Nevertheless, the optical integrity of the N-protected-α-aminoaldehyde seems to be sensitive to the reaction conditions. Pentacylic structures, having an anti C3-C11 backbone stereochemistry, were obtained from cyclization para- and ortho- to the 3-OH group of the l-DOPA derivative.     

A novel dynamic kinetic resolution accompanied by intramolecular transesterification: asymmetric synthesis of a 4-hydroxymethyl-2-oxazolidinone from serinol derivatives

Reaction paths of the one-pot reaction of (R)-2-(α-methylbenzyl)amino-1,3-propanediol (1) and 2-chloroethyl chloroformate with DBU giving (4S,αR)-4-hydroxymethyl-3-(α-methylbenzyl)-2-oxazolidinone [(4S)-2] (94% de) were investigated. Intermediates of this reaction, 2-chloroethyl (2S)- and 2-chloroethyl (2R)-3-hydroxy-2-[(αR)-α-methylbenzyl]aminopropyl carbonates [(2S)-4 and (2R)-4], were synthesized individually. After the addition of DBU to the respective solution of the carbonate (2S)-4 and that of (2R)-4 in dichloromethane, the intramolecular transesterification between (2S)-4 and (2R)-4 and the diastereoselective intramolecular cyclization proceeded to afford (4S)-2 in high diastereomeric excess. Therefore, two monocarbonates (2S)-4 and (2R)-4 were kinetically resolved by this cyclization during the intramolecular transesterification between (2S)-4 and (2R)-4. We found that this process involved dynamic kinetic resolution accompanied by intramolecular transesterification.     

Copolymerization of N,N-diallyl-N,N-dimethylammonium chloride with ethylene glycol vinyl ether in aqueous medium

The radical copolymerization of N,N-diallyl-N,N-dimethylammonium chloride (AMAC) (M₁) with ethylene glycol vinyl ether (M₂) in an aqueous medium proceeds at a high rate to afford random copolymers. The reactivity ratios equal to r ₁ = 2.18 and r ₂ = 0.01 indicate that AMAC is a more active comonomer. The overall reaction order in comonomers is 2.4, and the effective activation energy is 97.4 ± 2 kJ/mol. The monomer M₁ enters into copolymerization by both of the double bonds with the formation of pyrrolidinium structures in the chain through the cyclization stage.     

A simple protocol to help calculate saddle points. Transition-state structures for the Meyer—Schuster reaction in non-aqueous media: An ab initio MO study

A simple procedure to help calculate transition-state (TS) structures of complex chemical systems is proposed and tested. For the cases studied in this laboratory, substantial gains in computer CPU time have been obtained. As an example, the TS structures for the intramolecular mechanism corresponding to the 1,3-hydroxyl shift occurring in (CH₃)₂C(OH) CCH is calculated. STO-3G, 4-31G and 4-21G basis sets have been used to represent the wavefunction of the ground electronic state. Invariance of the present TS structure to changes in basis set has been found.     

Analysis of Menger’s ‘spatiotemporal hypothesis’

Ab initio at HF/6-31G and HF/6-31G(d,p) levels, AM1 and molecular mechanics calculations of thermodynamic and kinetic parameters for Menger’s system 1-3 (an important enzyme model) indicate that the remarkable enhancement in the proton transfer process is largely the result of a strain effect, and this strain is a function of the bond distance between the two reacting centers and the value of the angle of attack.     

NaNO2/I2 as an alternative reagent for the synthesis of 1,2,3-benzotriazin-4(3H)-ones from 2-aminobenzamides

An efficient transformation of 2-aminobenzamides to 1,2,3-benzotriazin-4(3H)-ones in the presence of sodium nitrite (NaNO₂) and Iodine (I₂) is described. The reaction is proposed to proceed via formation of nitrosyl halide that induces nitrosylation of the amino group of 2-aminobenzamide leading to diazotization followed by intramolecular cyclization.     

Synthesis of cyclic peptides via O-N-acyl migration

We describe here a novel and convenient synthesis of head-to-tail cyclic peptide avoiding racemization. Linear depsipeptides including a serine residue as the key element for ester bond formation and acyl transfer were synthesized on 2-chlorotrityl chloride resin. After cleavage from the resin, intramolecular head-to-tail cyclization was performed in solution by C-terminal activation of urethane protected O-acyl serine residue. After removal of the N^α-serine protecting group, the final step consisted in O-N-acyl migration reaction on the ‘switch’ or ‘click’ element to restore native cyclic peptides.     

Functionalization of Csp-H bond—Sc(OTf)3-catalyzed domino 1,5-hydride shift/cyclization/Friedel-Crafts acylation reaction of benzylidene Meldrum’s acids

Under Sc(OTf)₃ catalysis, benzylidene Meldrum’s acids bearing a tethered p-methoxyphenethyl group were observed to undergo a [1,5]-hydride shift/cyclization at room temperature, representing a mild Csp³-H bond functionalization. The resulting spiro Meldrum’s acid intermediates then underwent intramolecular Friedel-Crafts acylation, completing the one-pot, domino reaction. The reported protocol generates the 6-6-5-6 tetracyclic core of tetrahydrobenzo[b]fluoren-11-ones.     

Rotamerisation and intramolecular proton transfer of 2-(2′-hydroxyphenyl)oxazole, 2-(2′-hydroxyphenyl)imidazole and 2-(2′-hydroxyphenyl)thiazole: a theoretical study

Semi-empirical (AM1-SCI) calculations have been performed on 2-(2′-hydroxyphenyl)oxazole (HPO), 2-(2′-hydroxyphenyl)imidazole (HPI) and 2-(2′-hydroxyphenyl)thiazole (HPT) to rationalise the photophysical behaviour of the compounds exhibiting intramolecular rotation as well as excited state intramolecular proton transfer (ESIPT). The calculations reveal that there is a gradual variation in the properties from HPO to HPT through HPI so far as the existence of the rotational isomers in the ground state is concerned. While HPO gives rise to two stable rotamers (I and II) in all the common solvents, there is only one stable species for HPT in the S₀ state. For HPI, rotamer II is possible only in the isolated state and/or in solvents of low polarity, but in high polar solvents it gives rise to the normal form (I) only. For all the molecules in the series, however, intramolecular proton transfer (IPT) takes place in the lowest excited singlet (S₁) and the triplet (T₁) states. Combination of the rotamerism and ESIPT gives rise to multiple fluorescence bands for the fluorophores. Theoretical assignments have been made for the excitation, fluorescence and phosphorescence bands. Simulated potential energy curves (PEC) in different electronic states reveal that the IPT process is feasible in either of the S₁ and T₁ states but not in the ground state. The ESIPT reaction has been found to be favoured both thermodynamically and kinetically in these electronic states compared to the ground state. However, quantum mechanical tunnelling has been proposed for the prototropic reaction to proceed in the excited states.     

Influence of steric parameters on the synthesis of tetramates from α-amino-β-alkoxy-esters and Ph3PCCO

α-Aminoesters react with Ph₃PCCO in a domino addition–Wittig cyclization sequence affording enantiomerically pure tetramates. In the case of β-oxo functionalized α-aminoesters, e.g., esters of serine, threonine or β-hydroxyornithine the yields of this reaction depend heavily on the bulkiness of the β-OR group and on the configuration of β-carbon atom C-3. Smaller residues and 2R/3R-configured aminoesters give better yields. The alkoxycarbonyl group of the ester moiety and the residue on the N-atom are less important. These findings can be accounted for by assuming an early puckered transition state for the intramolecular ring-closing Wittig reaction. The addition of sub-stoichiometric amounts of benzoic acid or N-hydroxysuccinimide (for acid-sensitive compounds) is advantageous in some cases as it accelerates the formation of the intermediate amide ylides.     

Molecular structure,vibrational spectra,first order hyper polarizability,NBO and HOMO–LUMO analysis of 4-amino-3(4-chlorophenyl) butanoic acid

The Fourier transform infrared (FT-IR) and Fourier transform Raman (FTR) spectra of 4-amino-3(4-chlorophenyl) butanoic acid were recorded in the regions 4000–400 cm⁻¹ and 4000–100 cm⁻¹, respectively, in the solid phase. Molecular electronic energy, geometrical structure, harmonic vibrational spectra, infrared intensities and Raman scattering activities, highest occupied molecular orbital, lowest unoccupied molecular orbital energy, energy gaps and thermodynamical properties such as zero-point vibrational energies, rotational constants, entropies and dipole moment were computed at the Hartree–Fock/6-31G(d,p) and three parameter hybrid functional Lee–Yang–Parr/6-31G(d,p) levels of theory. The vibrational studies were interpreted in terms of potential energy distribution (PED). The results were compared with experimental values with the help of scaling procedures. Most of the modes have wave numbers in the expected range and are in good agreement with computed values. The first order hyperpolarizability (β_total) of this molecular system and related properties (β, μ, 〈α〉 and Δα) are calculated using HF/6-31G(d,p) and B3LYP/6-31G(d,p) methods based on the finite-field approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond-like weak interaction has been analyzed using natural bond orbital (NBO) analysis by using B3LYP/6-31G(d,p) method. The results show that electron density (ED) in the σ1 and π1 antibonding orbitals and second-order delocalization energies E⁽²⁾ confirm the occurrence of intramolecular charge transfer (ICT) within the molecule.     

A novel one-pot synthesis of 2-arylpyrazoloquinolinone derivatives

Two regioisomers of 2-arylpyrazolo[3,4-c]quinolin-4(5H)-ones and 2-arylpyrazolo[4,3-c]quinolin-4(5H)-ones were synthesized by utilizing 3-arylsydnones, ethyl 3-bromopropynoate, and 2-aminophenylboronic acid pinacol ester in presence of catalytic agent Pd(PPh₃)₄. This efficient one-pot synthesis methodology involved 1,3-dipolar cycloaddition, Suzuki coupling reaction, and intramolecular cyclization three sequence steps.