Ethylenediamine Catalyzed Decarboxylation of Oxaloacetic Acid: A DFT Investigation

2013 ◽  
Vol 781-784 ◽  
pp. 253-258
Author(s):  
Ming Zhi Song ◽  
Zai Long Zhang ◽  
Chuan Gang Fan ◽  
Da Zhi Li ◽  
Shi Guo Zhang
Keyword(s):  
Gas Phase ◽  
Energy Barrier ◽  
Density Functional ◽  
Water Solution ◽  
Membered Ring ◽  
Transition Structure ◽  
Functional Theory ◽  
Oxaloacetic Acid ◽  
Stepwise Mechanism ◽  
Rate Determining Step

The decarboxylation mechanism of oxaloacetic acid aided with ethylenediamine or without any catalyst is investigated employing Density Functional Theory (DFT). DFT calculations for both the gas phase and in water solution indicate a stepwise mechanism for each of the steps of the reactions. In the catalyzed mechanism, the dehydration of carbinolamine (IM1) is via a seven-membered ring transition structure (TS5), which is consistent with the structure proposed by Thalji, et al. The decarboxylation of the imine (IM6) is the rate determining step with an energy barrier of 16.46 kcal/mol, lower than the reaction without any catalysts or catalyzed with ions.

THEORETICAL INVESTIGATION ON THE REACTION MECHANISM OF CuI-CATALYZED FORMATION OF ETHYL 2-PHENYLACETOACETATE

2009 ◽  
Vol 08 (supp01) ◽  
pp. 1087-1098
Author(s):  
LAI-CAI LI ◽  
YING ZHANG ◽  
AN-MIN TIAN ◽  
NING-BEW WONG
Keyword(s):  
Reaction Mechanism ◽  
Gas Phase ◽  
Energy Barrier ◽  
Density Functional ◽  
Catalytic Mechanism ◽  
Functional Theory ◽  
Nonlocal Correlation ◽  
Rate Determining Step ◽  
Stage 1 ◽  
Two Stages

The reaction mechanism of CuI -catalyzed formation of ethyl 2-phenylacetoacetate by arylation of ethyl acetoacetate has been investigated by density functional theory (DFT) using Becke's three-parameter nonlocal exchange functional and the Lee, Yang, and Parr nonlocal correlation functional (B3LYP). The geometries of the reactants, intermediates, transition states, and products have been optimized and verified by means of vibration frequency calculations. According to our assumption, this reaction can be divided into two stages. The rate-determining step is found to be the 3 → 4-TS procedure, which is the first procedure of stage 1. The low energy barrier of 39.85 kcal/mol indicates that this reaction can be carried out, which is in accordance with the experimental facts. For comparison, we have investigated the reaction mechanism of the same chemical reaction without CuI catalyst, whose energy barrier of rate-determining step is 212.76 kcal/mol higher than that with CuI catalyst. This fact suggests that CuI catalyst accelerates the reaction by remarkably lowering the energy barrier. The solvation effects on the barriers of the reaction are important. But the energetic order in DMSO solvent seems to be almost the same as that in gas-phase, which indicates that our conclusion achieved in gas-phase is believable. Our findings reveal the microscopic catalytic mechanism of CuI and are in agreement with the experimental facts.

Exploring chemistry features of favipiravir in octanol/water solutions

2021 ◽  
pp. 1-12
Author(s):  
Halimeh Rajabzadeh ◽  
Ayla Sharafat ◽  
Maryam Abbasi ◽  
Maryam Eslami Gharaati ◽  
Iraj Alipourfard
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Partition Coefficients ◽  
Density Functional ◽  
Water Solution ◽  
Peptide Group ◽  
Functional Theory ◽  
Water Solutions ◽  
Group Rotations ◽  
Heterocyclic Structure

Favipiravir (Fav) has become a well-known drug for medication of patients by appearance of COVID-19. Heterocyclic structure and connected peptide group could make changes for Fav yielding different features from those required features. Therefore, it is indeed a challenging task to prepare a Fav compound with specific features of desired function. In this work, existence of eight Fav structures by tautomeric formations and peptide group rotations were obtained using density functional theory (DFT) optimization calculations. Gas phase, octanol solution, and water solution were employed to show impact of solution on features of Fav besides obtaining partition coefficients (LogP) for Fav compounds. Significant impacts of solutions were seen on features of Fav with the obtained LogP order: Fav-7 >  Fav-8 >  Fav-4 >  Fav-3 >  Fav-2 >  Fav-5 >  Fav-1 >  Fav-6. As a consequence, internal changes yielded significant impacts on features of Fav affirming its carful medication of COVID-19 patients.

A DFT study on the mechanism of reaction between 2, 4-diisocyanatotolune and cellulose

2016 ◽  
Vol 15 (02) ◽  
pp. 1650012 ◽  
Author(s):  
Jiping Cao ◽  
Yali Liu ◽  
Aijuan Shi ◽  
Yuan Yuan ◽  
Mingliang Wang
Keyword(s):  
Reaction Mechanisms ◽  
Energy Barrier ◽  
Density Functional ◽  
Membered Ring ◽  
Functional Theory ◽  
Mechanism Of Reaction ◽  
The Density Functional Theory ◽  
Good Accordance ◽  
Experimental Activation Energy ◽  
Ring Transition State

The reaction mechanisms between 2, 4-Diisocyanatotolune (2, 4-TDI) and cellulose have been investigated using the density functional theory at the B3LYP/6-31[Formula: see text]G (d, p) level. The calculations show that the direct addition of 2, 4-TDI and cellulose possesses an unrealistically high barrier of 32–34[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. With a neighboring [Formula: see text]-d-glucose serving as a proton transporter by forming a flexible six-membered ring transition state, the energy barrier of the reaction is significantly reduced to 16–18 kcal[Formula: see text]mol[Formula: see text], which is in a good accordance with the experimental activation energy of 13.9–16.7[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is indicated that the reaction between 2, 4-TDI and cellulose is auto-catalyzed with a neighboring [Formula: see text]-d-glucose acting as a reactive catalyst.

scholarly journals Ensemble Effects of Explicit Solvation on Allylic Oxidation

2021 ◽  
Author(s):  
Hung Le ◽  
Mariano Guagliardo ◽  
Anne Gorden ◽  
Aurora Clark
Keyword(s):  
Gas Phase ◽  
Energy Barrier ◽  
Density Functional ◽  
Umbrella Sampling ◽  
Catalytic Cycle ◽  
Allylic Oxidation ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Ensemble Effects ◽  
Explicit Solvation

<div>Umbrella-sampling density functional theory molecular dynamics (DFT-MD) has been employed to study the full catalytic cycle of the allylic oxidation of cyclohexene</div><div>using a Cu(II) (E)-6-amino-7-((2-hydroxybenzylidene)amino)quinoxalin-2-ol complex in acetonitrile, which creates the desired cyclohexenone and H 2 O as products. In comparison to prior study using gas-phase DFT, a significant solvent effect is observed on the rate determining allylic H-atom abstraction step (which has a free energy barrier of 12.1 ± 0.2 kcal/mol). During the cycle, the explicit solvation and ensemble sampling of solvent configurations reveals an important dehydrogenation and re-hydrogenation step of the -NH 2 ligand that is essential to catalyst recovery. This work illustrates the importance of ensemble solvent configurational sampling to reveal the breadth of processes that underpin the full catalytic cycle.</div>

scholarly journals Ensemble Effects of Explicit Solvation on Allylic Oxidation

2021 ◽  
Author(s):  
Hung Le ◽  
Mariano Guagliardo ◽  
Anne Gorden ◽  
Aurora Clark
Keyword(s):  
Gas Phase ◽  
Energy Barrier ◽  
Density Functional ◽  
Umbrella Sampling ◽  
Catalytic Cycle ◽  
Allylic Oxidation ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Ensemble Effects ◽  
Explicit Solvation

<div>Umbrella-sampling density functional theory molecular dynamics (DFT-MD) has been employed to study the full catalytic cycle of the allylic oxidation of cyclohexene</div><div>using a Cu(II) (E)-6-amino-7-((2-hydroxybenzylidene)amino)quinoxalin-2-ol complex in acetonitrile, which creates the desired cyclohexenone and H 2 O as products. In comparison to prior study using gas-phase DFT, a significant solvent effect is observed on the rate determining allylic H-atom abstraction step (which has a free energy barrier of 12.1 ± 0.2 kcal/mol). During the cycle, the explicit solvation and ensemble sampling of solvent configurations reveals an important dehydrogenation and re-hydrogenation step of the -NH 2 ligand that is essential to catalyst recovery. This work illustrates the importance of ensemble solvent configurational sampling to reveal the breadth of processes that underpin the full catalytic cycle.</div>

Theoretical Study on Aggregation of Nuclei-Containing Gas Phase

2017 ◽  
Author(s):  
Zhong Lan ◽  
Quan Xue ◽  
Xuehu Ma ◽  
Di Wang ◽  
Kejian Cao ◽  
...  
Keyword(s):  
Water Molecule ◽  
Gas Phase ◽  
Energy Barrier ◽  
Density Functional ◽  
Water Clusters ◽  
Condensation Nucleus ◽  
Condensation Process ◽  
Functional Theory ◽  
Particle Properties ◽  
Molecule Aggregation

Haze is a kind of typical heterogeneous nucleation phenomenon in gas phase condensation process. The existence of dust nucleus may induce water molecule aggregation among vapor phase under a certain humidity. In this article, we try to use Density Functional Theory simulation to explore the evolution mechanism of water molecule aggregation influenced by condensation nucleus from the perspective of molecules assembling. We can get the following results: the subcooling degree and physicochemical properties of nucleation center affect the hydrogen bond within the water clusters and the transformation energy barrier of water molecule aggregation tendency. Water vapor begins to heterogeneously condense or forms aggregation humidity in a certain condition based on the center of condensation nuclei. The analysis shows that the effect law of the degree and scale of aggregation or phase transition are influenced by the change of gas phase partial pressure, supersaturated degree along with particle properties. As the energy barrier of nucleation free energy decreases, the formation of water clusters will be easier.

scholarly journals Ensemble Effects of Explicit Solvation on Allylic Oxidation

2021 ◽  
Author(s):  
Hung Le ◽  
Mariano Guagliardo ◽  
Anne Gorden ◽  
Aurora Clark
Keyword(s):  
Gas Phase ◽  
Energy Barrier ◽  
Density Functional ◽  
Umbrella Sampling ◽  
Catalytic Cycle ◽  
Allylic Oxidation ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Ensemble Effects ◽  
Explicit Solvation

Umbrella-sampling density functional theory molecular dynamics (DFT-MD) has been employed to study the full catalytic cycle of the allylic oxidation of cyclohexene using a Cu(II) 7-amino-6-((2-hydroxybenzylidene)amino)quinoxalin-2-ol complex in acetonitrile to create cyclohexenone and H$_2$O as products. In comparison to gas-phase DFT, the solvent effect is observed as the rate determining allylic H-atom abstraction step has a free energy barrier of 12.1 $\pm$ 0.2 kcal/mol in solution. During the cycle, the explicit solvation and ensemble sampling of solvent configurations reveals important dehydrogenation and re-hydrogenation steps of the -NH$_2$ group bound to the Cu-site that are essential to catalyst recovery. This work illustrates the importance of ensemble solvent configurational sampling to reveal the breadth of processes that underpin the full catalytic cycle.<br>

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.

DFT study on the hydrolysis of metsulfuron-methyl: A sulfonylurea herbicide

2018 ◽  
Vol 17 (08) ◽  
pp. 1850050 ◽  
Author(s):  
Qiuhan Luo ◽  
Gang Li ◽  
Junping Xiao ◽  
Chunhui Yin ◽  
Yahui He ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Molecule ◽  
Carbonyl Group ◽  
Energy Barrier ◽  
Density Functional ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Metsulfuron Methyl ◽  
Catalytic Role ◽  
Hydrolysis Of

Sulfonylureas are an important group of herbicides widely used for a range of weeds and grasses control particularly in cereals. However, some of them tend to persist for years in environments. Hydrolysis is the primary pathway for their degradation. To understand the hydrolysis behavior of sulfonylurea herbicides, the hydrolysis mechanism of metsulfuron-methyl, a typical sulfonylurea, was investigated using density functional theory (DFT) at the B3LYP/6-31[Formula: see text]G(d,p) level. The hydrolysis of metsulfuron-methyl resembles nucleophilic substitution by a water molecule attacking the carbonyl group from aryl side (pathway a) or from heterocycle side (pathway b). In the direct hydrolysis, the carbonyl group is directly attacked by one water molecule to form benzene sulfonamide or heterocyclic amine; the free energy barrier is about 52–58[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. In the autocatalytic hydrolysis, with the second water molecule acting as a catalyst, the free energy barrier, which is about 43–45[Formula: see text]kcal[Formula: see text]mol[Formula: see text], is remarkably reduced by about 11[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is obvious that water molecules play a significant catalytic role during the hydrolysis of sulfonylureas.

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