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>

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>

Ensemble Effects on Allylic Oxidation within Explicit Solvation Environments

2021 ◽  
Author(s):  
Hung Minh Le ◽  
Mariano Guagliardo ◽  
Anne E. V. Gorden ◽  
Aurora Clark
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Density Functional ◽  
Umbrella Sampling ◽  
Catalytic Cycle ◽  
Allylic Oxidation ◽  
Functional Theory ◽  
Sampling Density ◽  
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...

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.

scholarly journals Mechanistic Insights into Selective Hydrogenation of C=C Bonds Catalyzed by CCC Cobalt Pincer Complexes: A DFT Study

Catalysts ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 168
Author(s):  
Zheng Zuo ◽  
Xinzheng Yang
Keyword(s):  
Energy Barrier ◽  
Density Functional ◽  
Pincer Complexes ◽  
Free Energy Barrier ◽  
Electronic Effects ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Hydrogenation Reactions ◽  
Catalytic Cycles ◽  
Hydrogenation Selectivity

The mechanistic insights into hydrogenations of hex-5-en-2-one, isoprene, and 4-vinylcyclohex-1-ene catalyzed by pincer (MesCCC)Co (Mes = bis(mesityl-benzimidazol-2-ylidene)phenyl) complexes are computationally investigated by using the density functional theory. Different from a previously proposed mechanism with a cobalt dihydrogen complex (MesCCC)Co-H2 as the catalyst, we found that its less stable dihydride isomer, (MesCCC)Co(H)2, is the real catalyst in those catalytic cycles. The generations of final products with H2 cleavages for the formations of C−H bonds are the turnover-limiting steps in all three hydrogenation reactions. We found that the hydrogenation selectivity of different C=C bonds in the same compound is dominated by the steric effects, while the hydrogenation selectivity of C=C and C=O bonds in the same compound could be primarily influenced by the electronic effects. In addition, the observed inhabition of the hydrogenation reactions by excessive addition of PPh3 could be explained by a 15.8 kcal/mol free energy barrier for the dissociation of PPh3 from the precatalyst.

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.

THE HYDROLYTIC DEAMINATION MECHANISM OF PROTONATED ADENINE: A DFT STUDY

2011 ◽  
Vol 10 (03) ◽  
pp. 309-320 ◽  
Author(s):  
XINLIN LIU ◽  
HUI ZENG ◽  
FANCUI MENG ◽  
JUNXIANG LIU
Keyword(s):  
Energy Barrier ◽  
Density Functional ◽  
Hydrogen Transfer ◽  
Density Functional Theory Method ◽  
Hydroxyl Group ◽  
Free Energy Barrier ◽  
Activation Energy Barrier ◽  
Functional Theory ◽  
Activation Free Energy ◽  
Hydrolytic Deamination

The hydrolytic deamination mechanism of protonated adenine has been studied using density functional theory method. There are five pathways according to adenine protonated at N1, N3 and N7, respectively. As for the N1 protonated adenine only one pathway has been found, while for N3 and N7 protonated adenine two pathways have been found. Pathway c2 is preferred due to lowest activation free energy barrier of 53.02 kcal/mol. In this pathway, the hydroxyl group of water attacks C6 atom and hydrogen atom attacks N10 atom to produce enol form of protonated hypoxanthine and ammonia, then hydrogen transfer occurs to cause enol-keto tautomerization of protonated hypoxanthine with the assistance of ammonia. Adenine deamination is easier to take place under acidic condition than under neutral condition owing to lower activation energy barrier.

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.

Effect of Substitution for Insertion of CO2 into Epoxides and Aziridines: An Ab Initio Study

2020 ◽  
Vol 73 (1) ◽  
pp. 30
Author(s):  
Yunhan Yang ◽  
Fenji Li ◽  
Cuicui Yang ◽  
Lijuan Jia ◽  
Lijuan Yang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Free Energy ◽  
Reaction Mechanism ◽  
Ab Initio ◽  
Energy Barrier ◽  
Density Functional ◽  
Free Energy Barrier ◽  
Ab Initio Study ◽  
Functional Theory ◽  
Concerted Mechanism

The insertion of CO2 into epoxides and aziridines has been studied using density functional theory (B3LYP) and ab initio (MP2) methods, and the effect of substitution for the two reactions are further explored. It is found that the reactivity of epoxides and aziridines are similar, and insertion of CO2 proceeds through a concerted mechanism. The substitutions of methyl and phenyl does not change the reaction mechanism, but the transition state for the substitution on the attacking position becomes loose with a lower free energy barrier. The substitutions of methyl and phenyl decrease the free energy barrier, with phenyl substitution having a greater affect. The results also show that the free energy barriers for the insertions of CO2 into aziridines are ~10kcalmol−1 lower than the corresponding reactions of CO2 with epoxides.

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.

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