Asymmetric Michael Addition Using Bifunctional Bicyclic Guanidine Organocatalyst: A Theoretical Perspective

2014 ◽  
Vol 67 (7) ◽  
pp. 1100 ◽  
Author(s):  
Ming Wah Wong ◽  
Aik Meng Eugene Ng
Keyword(s):  
Transition State ◽  
Michael Addition ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Catalytic Mechanism ◽  
Theoretical Perspective ◽  
Experimental Result ◽  
Dimethyl Malonate ◽  
Bond Forming ◽  
Asymmetric Michael Addition

To illustrate the general principle of asymmetric organocatalysis of chiral bicyclic guanidine, a density functional theory study was carried out to examine the catalytic mechanism, activation mode, origin of stereoselectivity of a [5,5]-bicyclic guanidine-catalyzed Michael addition of dimethyl malonate to 2-cyclopenten-1-one. Two types of bifunctional activation modes were examined: Brønsted acid and Brønsted-Lewis acid. The calculated enantioselectivity (ee), based on eight C–C bond forming transition states and their pre-transition state complexes, is in excellent accord with experimental result. The ternary pre-transition state complexes are stable species, which strongly influence the stereoselectivity. Similar to enzyme catalysis, the bicyclic guanidinium catalyst plays an essential recognition role in assembling the substrates together via hydrogen bonds, multiple C–H···O interactions (as oxyanion hole), donor–acceptor, and electrostatic interactions.

THEORETICAL MECHANISMS AND KINETICS FOR THE REACTION OF DIMETHYL SULFIDE AND OZONE IN WATER VAPOR

2005 ◽  
Vol 04 (04) ◽  
pp. 1101-1117 ◽  
Author(s):  
ANGELA SHIH ◽  
CALINA CIOBANU ◽  
FU-MING TAO
Keyword(s):  
Water Vapor ◽  
Transition State ◽  
Rate Constants ◽  
Energy Barrier ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
State Theory ◽  
Second Order ◽  
Water Molecules ◽  
Phase Reaction

The reaction mechanisms and kinetics for DMS + O 3 ⇒ DMSO + O 2 in water vapor are studied using density functional theory. A series of reaction pathways are determined with molecular clusters containing the reacting species and up to three water molecules. The results show that the energy barrier, defined as the energy difference between the reactant complex and the transition state, decreases progressively as each water molecule is added to the reacting system. A decreasing energy barrier is attributed to favorable electrostatic interactions between the reacting species and water at the transition state and at the more polar product. Rate constants for the second-order reactions, involving different combinations of hydrated reactants up to three water molecules, are calculated using transition state theory with Eckart tunneling corrections. Effective rate constants for DMS + O 3 ⇒ DMSO + O 2 are obtained using the calculated second-order rate constants and the concentrations of hydrated reactants present in saturated water vapor. The results show that the rate of reaction for DMS + O 3 ⇒ DMSO + O 2 increases dramatically in the presence of water vapor, by up to seven orders of magnitude for reactions involving three water molecules. The study implies that the gas-phase reaction of DMS with ozone is significant in the troposphere and can greatly influence the global climate.

Pentanidium-Catalyzed Asymmetric Phase-Transfer Conjugate Addition: Prediction of Stereoselectivity via DFT Calculations and Docking Sampling of Transition States, and Origin of Stereoselectivity

2016 ◽  
Vol 69 (9) ◽  
pp. 983 ◽  
Author(s):  
Choon Wee Kee ◽  
Ming Wah Wong
Keyword(s):  
Density Functional ◽  
Catalytic Mechanism ◽  
Phase Transfer ◽  
Interaction Analysis ◽  
Hybrid Approach ◽  
Transition States ◽  
Interaction Model ◽  
Conjugate Addition ◽  
Experimental Result ◽  
Covalent Interaction

Density functional theory (DFT) study, at the M06–2X/6–311+G(d,p)//M06–2X/6–31G(d,p) level, was carried out to examine the catalytic mechanism and origin of stereoselectivity of pentanidium-catalyzed asymmetric phase-transfer conjugate addition. We employed a hybrid approach by combining automated conformation generation through molecular docking followed by subsequent DFT calculation to locate various possible transition states for the enantioselective conjugate addition. The calculated enantioselectivity (enantiomeric excess), based on the key diastereomeric C–C bond-forming transition states, is in good accord with experimental result. Non-covalent interaction analysis of the key transition states reveals extensive non-covalent interactions, including aromatic interactions, hydrogen bonds, and non-classical C–H⋯O interactions between the pentanidium catalyst and substrates. The origin of stereoselectivity was analysed using a strain-interaction model.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

scholarly journals Discovery of exolytic heparinases and their catalytic mechanism and potential application

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qingdong Zhang ◽  
Hai-Yan Cao ◽  
Lin Wei ◽  
Danrong Lu ◽  
Min Du ◽  
...  
Keyword(s):  
Heparan Sulfate ◽  
Structural Study ◽  
Enzyme Activities ◽  
Potential Application ◽  
Electrostatic Interactions ◽  
Catalytic Mechanism ◽  
Functional Studies ◽  
Research Gap ◽  
Sequential Digestion

AbstractHeparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.

scholarly journals Adsorption and Desorption Mechanisms of Rare Earth Elements (REEs) by Layered Double Hydroxide (LDH) Modified with Chelating Agents

2019 ◽  
Vol 9 (22) ◽  
pp. 4805 ◽  
Author(s):  
Shuang Zhang ◽  
Naoki Kano ◽  
Kenji Mishima ◽  
Hirokazu Okawa
Keyword(s):  
Rare Earth ◽  
Quantum Chemistry ◽  
Rare Earth Elements ◽  
Adsorption Capacity ◽  
Density Functional ◽  
Stable State ◽  
Experimental Result ◽  
Adsorption And Desorption ◽  
Adsorption Affinity ◽  
Quantum Chemistry Calculations

In order to obtain the adsorption mechanism and adsorption structures of Rare Earth Elements (REEs) ions adsorbed onto layered double hydroxides (LDH), the adsorption performance of LDH and ethylenediaminetetraacetic acid (EDTA) intercalated LDH for REEs was investigated by batch experiments and regeneration studies. In addition to adsorption capacity, the partition coefficient (PC) was also evaluated to assess their true performance metrics. The adsorption capacity of LDH increases from 24.9 μg·g−1 to 145 μg·g−1 for Eu, and from 20.8 μg·g−1 to 124 μg·g−1 for La by intercalating EDTA in this work; and PC increases from 45.5 μg·g−1·uM−1 to 834 μg·g−1·uM−1 for Eu, and from 33.6 μg·g−1·μM−1 to 405 μg·g−1·μM−1 for La. Comparison of the data indicates that the adsorption affinity of EDTA-intercalated LDH is better than that of precursor LDH no matter whether the concept of adsorption capacity or that of the PC was used. The prepared adsorbent was characterized by XRD, SEM-EDS and FT-IR techniques. Moreover, quantum chemistry calculations were also performed using the GAUSSIAN09 program package. In this calculation, the molecular locally stable state structures were optimized by density functional theory (DFT). Both the quantum chemistry calculations and the experimental data showed that REEs ions adsorbed by EDTA-intercalated LDH are more stable than those adsorbed by precursor LDH. Furthermore, the calculation results of adsorption and desorption rates show that adsorption rates are larger for Eu(III) than for La(III), which agrees with the experimental result that Eu(III) has a higher adsorption ability under the same conditions. The LDHs synthesized in this work have a high affinity for removing REEs ions.

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