Is acyl migration to the aglycon avoidable in 2-acyl assisted glycosylation reactions?

2004 ◽  
Vol 82 (7) ◽  
pp. 1157-1171 ◽  
Author(s):  
Attila Bérces ◽  
Dennis M Whitfield ◽  
Tomoo Nukada ◽  
Iwona do Santos Z. ◽  
Agnes Obuchowska ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Dft Calculations ◽  
Density Functional ◽  
Acyl Migration ◽  
Carbonyl Oxygen ◽  
Acyl Transfer ◽  
Protecting Group ◽  
Neighboring Group ◽  
Bond Forming ◽  
Anomeric Carbon

This report unequivocally separates orthoester formation from acyl transfer for the first time and indicates possible routes to eliminate 2-O-acyl transfer during glycosylation reactions. Experimental evidence is shown that acyl transfer from 2-O-acyl-3,4,6-tri-O-benzyl-D-galactopyranose-derived glycosyl donors decreases in the order formyl > acetyl > pivaloyl. The 2-O-benzoyl derivatives are more variable, in some cases transferring easily, and in others not at all. Density functional theory (DFT) calculations of the structure and energetics of dioxolenium ion and related intermediates suggest that a proton transfer pathway from the nucleophile to O-2 provides an explanation for the observed trends. These DFT calculations of the proton transfer pathway support a mechanism in which a relay molecule is involved. Further DFT calculations used a constraint based on linear combinations of six bond lengths to establish the sequence of bond breaking and bond forming. The calculated anomeric carbon to former carbonyl oxygen bond that breaks during acyl transfer is the longest in the formyl case and shortest in those that exhibit little or no acyl transfer. Rotation about the aromatic to carbonyl Ph—C(=O) bond is different from the alkyl series. Analysis of this proposed TS led to the postulate that 2,6-substitution may hinder rotation even more. Thus, the 2,6-dimethylbenzoyl analogue was synthesized and it does not transfer directly or by rearrangement of its readily formed orthoester. DFT calculations suggested that 2,6-dimethoxybenzoyl should also not transfer easily. Experimentally, this proved to be the case and this new 2-O-acyl protecting group cleaves at 50 °C with a 1 mol/L solution of LiOH in methanol. Thus, a calculated transition state has led to a prototype of a protecting group that solves a major problem in oligosaccharide synthesis.Key words: glycosylation, carbohydrates, quantum chemistry, reaction mechanism, neighboring-group effects.

scholarly journals Decarboxylation versus Acetonitrile Loss in Silver Acetate and Silver Propiolate Complexes, [RCO2Ag2(CH3CN)n]+ (where R = CH3 and CH3C≡C; n = 1 and 2)

2015 ◽  
Vol 68 (9) ◽  
pp. 1385 ◽  
Author(s):  
Jiawei Li ◽  
George N. Khairallah ◽  
Richard A. J. O'Hair
Keyword(s):  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Ion Trap ◽  
Fragmentation Pathway ◽  
Binding Energies ◽  
Silver Acetate ◽  
Bond Forming ◽  
Fragmentation Reactions ◽  
A Minor

Gas-phase experiments using collision-induced dissociation in an ion trap mass spectrometer have been used in combination with density functional theory (DFT) calculations (at the B3LYP/SDD6–31+G(d) level of theory) to examine the competition between decarboxylation and loss of a coordinated acetonitrile in the unimolecular fragmentation reactions of the silver acetate and silver propiolate complexes, [RCO2Ag2(CH3CN)n]+ (where R = CH3 and CH3C≡C; n = 1 and 2), introduced into the gas-phase via electrospray ionisation. When R = CH3, loss of acetonitrile is the sole reaction channel observed for both complexes (n = 1 and 2), consistent with DFT calculations, which highlight that the barriers for decarboxylation 2.18 eV (n = 2) and 1.96 eV (n = 1) are greater than the binding energies of the coordinated acetonitriles (1.60 eV for n = 2; 1.64 eV for n = 1). In contrast, when R = CH3C≡C, decarboxylation is the main fragmentation pathway observed for both complexes (n = 1 and 2), with loss of acetonitrile only being a minor product channel. This is consistent with DFT calculations, which reveal that the barriers for decarboxylation are 1.17 eV (n = 2) and 1.16 eV (n = 1), which are both below the binding energies of the coordinated acetonitriles (1.55 eV for n = 2; 1.56 eV for n = 1). The barrier for decarboxylation of [CH3C≡CCO2Ag2]+ is 1.22 eV, which is less than the 2.06 eV reported for decarboxylation of [CH3CO2Ag2]+ (Al Sharif et al. Organometallics, 2013, 32, 5416). The observed ease of decarboxylation of silver propiolate complexes in the gas-phase is consistent with the recently reported use of silver salts in metal catalysed decarboxylative C–C and C–X bond forming reactions of propiolic acids.

scholarly journals Crystal structure, spectral characterization, molecular modeling studies and structural effects of the proton transfer process for (E)-5-methoxy-2-[(3,4-dimethylphenylimino) methyl]phenol

2017 ◽  
Vol 36 (2) ◽  
pp. 265
Author(s):  
Basak Kosar Kirca ◽  
Gonca Ozdemir Tarı ◽  
Cıgdem Albayrak Kastas ◽  
Mustafa Odabasoglu ◽  
Orhan Buyukgungor
Keyword(s):  
Proton Transfer ◽  
Dft Calculations ◽  
Density Functional ◽  
Tautomeric Form ◽  
Bond Distance ◽  
Molecular Geometry ◽  
Spectroscopic Properties ◽  
Intramolecular Proton Transfer ◽  
X Ray ◽  
Pes Scan

The main purpose of this study is to characterize a new organic material, (E)-5-methoxy-2-[(3,4-dimethylphenylimino)methyl]phenol, which was synthesized and grown as a single crystal. The molecular structure and spectroscopic properties of the ortho-hydroxy Schiff base compound were determined by X-ray diffraction analysis, Fourier-transform infrared (FT-IR), ultraviolet-visible (UV-Vis) and nuclear magnetic resonance (NMR) spectroscopy techniques, experimentally and computationally with density functional theory (DFT) calculations. X-ray and UV-Vis studies show that the compound exists in an OH tautomeric form in the solid and solvent media. The gas phase geometry optimizations of two possible forms of the title compound, resulting from the prototropic tautomerism, were obtained using DFT calculations at the B3LYP/6-311G+(d,p) level of theory. A relaxed potential energy surface (PES) scan was performed based on the optimized geometry of the OH tautomeric form by varying the redundant internal coordinate, the O-H bond distance. According to the PES scan process, the molecular geometry is strongly affected by the intramolecular proton transfer. The calculated first hyperpolarizability indicates that the compound could be a good material for non-linear optical applications. 

scholarly journals Dual-Function Enzyme Catalysis for Enantioselective Carbon–Nitrogen Bond Formation

2021 ◽  
Author(s):  
zhen liu ◽  
Carla Calvó-Tusell ◽  
Andrew Z. Zhou ◽  
kai chen ◽  
Marc Garcia-Borràs ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Active Site ◽  
Density Functional ◽  
Dual Function ◽  
Cytochrome P450 Enzymes ◽  
Active Site Residues ◽  
Bond Forming ◽  
Enzymatic Transformation ◽  
Excellent Activity ◽  
Dynamics Simulations

<p>Whereas enzymatic asymmetric carbene N–H insertion is a powerful method for preparation of chiral amines in principle, it has suffered from limited enantioselectivity in practice. In this work, we demonstrate that engineered cytochrome P450 enzymes can catalyze this abiological C–N bond-forming reaction with excellent activity and selectivity (up to 32,100 TTN, >99% yield and 98% e.e.) to prepare a series of bioactive <i>α</i>-amino lactones, which have not been accessed previously using a carbene insertion strategy. The enzymes are dual-function catalysts, effecting both carbene transfer and enantioselective proton-transfer catalysis, in a single active site. To gain insight into the mechanism of the enzymatic transformation, especially in the asymmetric protonation step, we performed extensive molecular dynamics simulations and density functional theory (DFT) calculations. Computational studies uncover the important roles of active-site residues that enable high activity and selectivity through interacting with the carbene intermediate and the amine substrate, and directing water molecules for selective proton transfer.<br></p><p></p>

scholarly journals Dual-Function Enzyme Catalysis for Enantioselective Carbon–Nitrogen Bond Formation

2021 ◽  
Author(s):  
zhen liu ◽  
Carla Calvó-Tusell ◽  
Andrew Z. Zhou ◽  
kai chen ◽  
Marc Garcia-Borràs ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Active Site ◽  
Density Functional ◽  
Dual Function ◽  
Cytochrome P450 Enzymes ◽  
Active Site Residues ◽  
Bond Forming ◽  
Enzymatic Transformation ◽  
Excellent Activity ◽  
Dynamics Simulations

<p>Whereas enzymatic asymmetric carbene N–H insertion is a powerful method for preparation of chiral amines in principle, it has suffered from limited enantioselectivity in practice. In this work, we demonstrate that engineered cytochrome P450 enzymes can catalyze this abiological C–N bond-forming reaction with excellent activity and selectivity (up to 32,100 TTN, >99% yield and 98% e.e.) to prepare a series of bioactive <i>α</i>-amino lactones, which have not been accessed previously using a carbene insertion strategy. The enzymes are dual-function catalysts, effecting both carbene transfer and enantioselective proton-transfer catalysis, in a single active site. To gain insight into the mechanism of the enzymatic transformation, especially in the asymmetric protonation step, we performed extensive molecular dynamics simulations and density functional theory (DFT) calculations. Computational studies uncover the important roles of active-site residues that enable high activity and selectivity through interacting with the carbene intermediate and the amine substrate, and directing water molecules for selective proton transfer.<br></p><p></p>

Highly enantioselective nitro-Mannich reaction of ketimines under phase-transfer catalysis

2017 ◽  
Vol 4 (7) ◽  
pp. 1266-1271 ◽  
Author(s):  
Bin Wang ◽  
Tong Xu ◽  
Lei Zhu ◽  
Yu Lan ◽  
Jingdong Wang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Dft Calculations ◽  
Transition State ◽  
Mannich Reaction ◽  
Density Functional ◽  
Phase Transfer Catalysis ◽  
Phase Transfer ◽  
Phase Transfer Catalyst ◽  
Protecting Group ◽  
Functional Theory

A novel bifunctional phase-transfer catalyst 1i was found to be highly efficient for the nitro-Mannich reaction of unactivated ketone-derived imines with the introduction of the protecting group 6-methyl-2-pyridylsulfonyl to the ketimines. Density functional theory (DFT) calculations are also performed to give the possible transition-state model.

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

Participation of 19-ester groups in the cleavage of 2α,3α- and 5α,6α-steroid epoxides. A case of competition between participation and external nucleophile attack

1979 ◽  
Vol 44 (5) ◽  
pp. 1496-1509 ◽  
Author(s):  
Pavel Kočovský ◽  
Václav Černý
Keyword(s):  
Perchloric Acid ◽  
Hydrobromic Acid ◽  
Ester Group ◽  
Carbonyl Oxygen ◽  
Cyclic Carbonate ◽  
Cyclic Ether ◽  
Normal Reaction ◽  
Neighboring Group ◽  
Ether Oxygen ◽  
The Difference

Acid cleavage of the acetoxy epoxide IIIa with aqueous perchloric acid or hydrobromic acid gave two types of products, i.e. the diol Va or the bromohydrin VIa, and the cyclic ether VIII. The latter compound arises by participation of ether oxygen of the ester group. On reaction with perchloric acid the epoxide IVa gave the diol XIIIa as a product of a normal reaction and the isomeric diol Xa as a product arising by intramolecular participation of the carbonyl oxygen of the 19-acetoxy group. Participation of the 19-ester group is confirmed by the formation of the cyclic carbonate XI when the 19-carbonate IVb is treated analogously. On reaction with hydrobromic acid, the epoxide IVa gave solely the bromohydrin XIVa as a product of the normal reaction course. Discussed is the similarity of these reactions with electrophilic additions to the related 19-acetoxy olefins I and II, the mechanism, the difference in behavior of both epoxides III and IV, the dependence of the product ratio on the nucleophility of the attacking species, and the competition between participation of an ambident neighboring group and an external nucleophile attack.

γ-Valerolactone-Introduced Controlled-Isomerization of Glucose for Lactic Acid Production over Sn-Beta Catalyst

2021 ◽  
Author(s):  
Xinpeng Zhao ◽  
Zhimin Zhou ◽  
hu luo ◽  
Yanfei Zhang ◽  
Wang Liu ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Lactic Acid ◽  
Dft Calculations ◽  
Acid Production ◽  
Density Functional ◽  
Lactic Acid Production ◽  
Hydrothermal Conversion ◽  
Functional Theory ◽  
Environment Friendly

Combined experiments and density functional theory (DFT) calculations provided insights into the role of the environment-friendly γ-valerolactone (GVL) as a solvent in the hydrothermal conversion of glucose into lactic acid...

Mechanistic understanding of the Cu(i)-catalyzed domino reaction constructing 1-aryl-1,2,3-triazole from electron-rich aryl bromide, alkyne, and sodium azide: a DFT study

2021 ◽  
Author(s):  
Hanlin Gan ◽  
Liang Peng ◽  
Feng Long Gu
Keyword(s):  
Density Functional Theory ◽  
Dft Calculations ◽  
Sodium Azide ◽  
Density Functional ◽  
Dft Study ◽  
Domino Reaction ◽  
Aryl Bromide ◽  
Functional Theory ◽  
Mechanistic Understanding

The mechanism of the Cu(i)-catalyzed domino reaction furnishing 1-aryl-1,2,3-triazole assisted by CuI and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) is explored with density functional theory (DFT) calculations.

scholarly journals Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

2021 ◽  
Vol 22 (15) ◽  
pp. 8033
Author(s):  
Aneta Jezierska ◽  
Kacper Błaziak ◽  
Sebastian Klahm ◽  
Arne Lüchow ◽  
Jarosław J. Panek
Keyword(s):  
Monte Carlo ◽  
Perturbation Theory ◽  
Potential Energy ◽  
Proton Transfer ◽  
Ir Spectra ◽  
Quantum Monte Carlo ◽  
Density Functional ◽  
Theoretical Approaches ◽  
Study Results ◽  
Intramolecular Hydrogen

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

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