scholarly journals Computational Studies on Water-Catalyzed Mechanisms for Stereoinversion of Glutarimide Intermediates Formed from Glutamic Acid Residues in Aqueous Phase

2019 ◽  
Vol 20 (10) ◽  
pp. 2410
Author(s):  
Tomoki Nakayoshi ◽  
Shuichi Fukuyoshi ◽  
Koichi Kato ◽  
Eiji Kurimoto ◽  
Akifumi Oda
Keyword(s):  
Glutamic Acid ◽  
Gas Phase ◽  
Aqueous Phase ◽  
Density Functional ◽  
Activation Barrier ◽  
Lower Probability ◽  
Activation Barriers ◽  
Functional Methods ◽  
Age Related ◽  
Calculated Activation

Aspartic acid (Asp) residues are prone to non-enzymatic stereoinversion, and Asp-residue stereoinversion is believed to be mediated via a succinimide (SI) intermediate. The stereoinverted Asp residues are believed to cause several age-related diseases. However, in peptides and proteins, few studies have reported the stereoinversion of glutamic acid (Glu) residues whose structures are similar to that of Asp. We previously presumed that Glu-residue stereoinversion proceeds via a glutarimide (GI) intermediate and showed that the calculated activation barriers of SI- and GI-intermediate stereoinversion are almost equivalent in the gas phase. In this study, we investigated the stereoinversion pathways of the l-GI intermediate in the aqueous phase using B3LYP density functional methods. The calculated activation barrier of l-GI-intermediate stereoinversion in the aqueous phase was approximately 36 kcal·mol−1, which was much higher than that in the gas phase. Additionally, as this activation barrier exceeded that of Asp-residue stereoinversion, it is presumed that Glu-residue stereoinversion has a lower probability of proceeding under physiological conditions than Asp-residue stereoinversion.

A density functional theory study on the performance of graphene and N-doped graphene supported Au3 cluster catalyst for acetylene hydrochlorination

2016 ◽  
Vol 94 (10) ◽  
pp. 842-847 ◽  
Author(s):  
Fei Zhao ◽  
Yang Wang ◽  
Lihua Kang
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Energy Gap ◽  
Activation Barrier ◽  
Similar Reaction ◽  
Functional Theory ◽  
Acetylene Hydrochlorination ◽  
Doped Graphene ◽  
Calculated Activation ◽  
Calculated Activation Barrier

Density functional theory (DFT) calculation was used to investigate the mechanism of Au3 clusters, separately supported on pure graphene (Au3/graphene) and one graphitic N-doped graphene (Au3/N-graphene). These supported Au3 clusters were used to catalyze acetylene hydrochlorination. Results show that the graphene supporter could obviously enhance the adsorption of reactants. Also, N-atom doping could broaden the energy gap between the HOMO of graphene and the LUMO of Au3, leading to the significantly attenuated interaction between the Au3 cluster and graphene by more than 19 kcal/mol (1 cal = 4.184 J). The two catalysts possessed extremely similar reaction mechanisms with activation energy values of 23.26 and 23.89 kcal/mol, respectively. The calculated activation barrier declined in the order of Au3 < Au3/N-graphene < Au3/graphene, suggesting that Au3/N-graphene could be a potential catalyst for acetylene hydrochlorination.

Twisted Push - Pull Ethylenes

2008 ◽  
Vol 61 (10) ◽  
pp. 805 ◽  
Author(s):  
Rakesh Naduvile Veedu ◽  
Paul V. Bernhardt ◽  
Rainer Koch ◽  
Curt Wentrup
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Room Temperature ◽  
Dihedral Angles ◽  
Functional Theory ◽  
Activation Barriers ◽  
Rapid Rotation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calculated Activation

As determined by X-ray crystallography, Meldrum’s acid derivatives 5, 6, and 8 feature dihedral angles around the central C5=C7 double bond of 14–35°, whereas for the anion 9 this angle is 90°. Density functional theory and MP2 calculations are in agreement with the experimental X-ray data for compounds 5–8, but for anion 9 an angle of only ~65° is predicted. It is concluded that a part of the torsion is due to packing forces in the crystal. It is further concluded that these molecules undergo rapid rotation about the central CC bonds at room temperature (calculated activation barriers 5–14 kcal mol–1).

Facile formation of azines from reactions of singlet methylene and dimethylcarbene with precursor diazirines: theoretical explorations

1999 ◽  
Vol 77 (5-6) ◽  
pp. 540-549 ◽  
Author(s):  
Gennady V Shustov ◽  
Michael TH Liu ◽  
K N Houk
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Ring Opening ◽  
Density Functional ◽  
Activation Barrier ◽  
Thermal Reaction ◽  
Orbital Theory ◽  
Functional Theory ◽  
Activation Barriers ◽  
Singlet Methylene

The reactions of the singlet methylene (1a) and dimethylcarbene (1b), with their diazirine precursors, diazirine (2a), and dimethyldiazirine (2b), have been studied theoretically using ab initio and density functional theory. The reaction has no activation barriers for the parent system (1a + 2a) and proceeds via a reactive complex and a transition state with a small negative enthalpy of activation Δ Hnot =298 = -1.1 kcal mol-1, ΔSnot =298 = -34.4 cal mol-1 K-1, ΔG°298 = 9.2 kcal mol-1) for the dimethyl derivatives (1b + 2b). The formation of N-methylene diazirinium ylides (3a,b) is exothermic by 64-80 kcal mol-1. The isomer, 1,3-diazabicyclo[1.1.0]butane (4a), is more stable (5-12 kcal mol-1) than isomer 3a, but can neither be formed by direct thermal reaction of 1a with 2a nor undergo the direct rearrangement into formaldazine (5a). The rearrangement of ylides 3a,b into azines 5a,b proceeds by conrotatory C3-N1 ring opening. The predicted activation barrier of ca. 15 kcal mol-1 for the ring opening in ylide 3b is in excellent agreement with experimental data. The formation of pyridinium ylides from carbenes and pyridine is also studied.Key words: diazirinium ylide, ab initio MO (molecular orbital) theory, density functional theory, pyridinium ylide, CIS (singles configuration interaction) transition energies.

scholarly journals Tautomeric Equilibrium Revisited: proton-tautomerism in solvent and the fundamentals of molecular stability prediction.

2019 ◽  
Author(s):  
Andre Ricardo Carvalho
Keyword(s):  
Gas Phase ◽  
Relative Stability ◽  
Density Functional ◽  
Software Tool ◽  
Tautomeric Equilibrium ◽  
Consistent Estimate ◽  
Methods Development ◽  
Functional Methods ◽  
Molecular Stability ◽  
Molecular Orbital Analysis

Understanding the molecular stability is important for predicting the relative reactivity of chemical agents and the relative yields of desirable products. However, over decades, a consistent estimate of a particular chemical equilibrium (proton-tautomerism) has proven challenging. We revisit the molecular orbital analysis in the classic tautomeric oxo-hydroxy case, i.e., 2-pyridone/2-hydroxypyridine in gas-phase and solution, (Wong et al. 1992). Our results indicate the possibility of tuning the tautomeric equilibrium through directing groups. Our findings also reveal the lack of <a></a>reproducibility of orbital energies as responsible for the remarkable contrast between the results of the wavefunction and density functional methods. Our proposal leads the correction in the estimation of relative stability in excellent agreement with experiments in gas-phase and solution. The analogous approach for different compounds corroborates the reliability of our description on the molecular stability and its potential application, e.g., a guide to estimate the relative stability of molecules, to measure the confidence of the proposed reaction mechanisms by different theoretical methods, development of the molecular switches and computer-aided drug design. A software tool for Gaussian 09 package, in the support information, is available on the author's ORCiD page.<br>

scholarly journals Theoretical study of dimethylcarbonate production by urea alcoholysis

2020 ◽  
Vol 62 (4) ◽  
pp. 38-50
Author(s):  
Nikita I. Kurshev ◽  
Keyword(s):  
Zinc Oxide ◽  
Density Functional ◽  
Dimethyl Carbonate ◽  
Activation Barrier ◽  
Equilibrium Constants ◽  
Density Functional Method ◽  
Intermediate Formation ◽  
Functional Method ◽  
Activation Barriers ◽  
The Difference

Using the density functional method М06, the mechanisms of non-catalytic reactions of transesterification of urea with methanol with the formation of dimethyl carbonate, as well as in catalysis with zinc oxide and acetate, were studied. The transesterification proceeds stepwise with the intermediate formation of methyl carbamate. The non-catalytic process of transesterification of urea with methanol proceeds by the mechanism of nucleophilic SN2 substitution and is accompanied by the formation of pre-reaction complexes, which through synchronous transition states turn into post-reaction complexes, decomposing into ammonia and methyl carbamate in the first stage and dimethyl carbonate in the second. It has been established that methanol associates can take part in these reactions. Their participation is preferable both kinetically and thermodynamically. An analysis of the equilibrium constants of the reaction of urea with methanol at various temperatures showed that in a wide temperature range their values remain large in the first stage – the formation of methyl carbamate and become significantly reversible in the second – the conversion of methyl carbamate to dimethyl carbonate. Reactions involving acetate and zinc oxide proceed through the same stages as non-catalytic interactions. In the case of zinc acetate catalyzed reactions, if methanol monomer is involved in the reaction, the reaction of formation of methyl carbamate has a lower activation barrier compared to the reaction of conversion of methyl carbamate to dimethyl carbonate. If a methanol dimer is involved in the reaction, both reactions have a practically equal activation barrier. In the case of zinc oxide catalyzed interactions, reactions involving a methanol dimer were not detected. The participation of the catalyst leads to a significant decrease in activation barriers, and a more significant decrease occurs in the case of catalysis with zinc oxide. The reason for the different catalytic activity, in our opinion, is the difference in the charges on the urea carbon atom in the pre-reaction complexes.

Carbon–hydrogen vs. carbon–halogen oxidative addition of chlorobenzene to a cationic iridium(I) system — A density functional theory study

2009 ◽  
Vol 87 (10) ◽  
pp. 1460-1469 ◽  
Author(s):  
Hong Wu ◽  
Michael B. Hall
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Activation Barrier ◽  
Experimental Results ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
System A ◽  
Oxidative Additions ◽  
Calculated Activation ◽  
Calculated Activation Barrier

Density functional theory (DFT) is used to explore the competitive C−H and C−Cl oxidative additions (OA) of chlorobenzene to the cationic Ir(I) complex: [(PNP*)IrI]+ [PNP* = 2,6-bis((dimethylphosphino)methyl)pyridine]. Consistent with experimental results, the calculated activation barrier for C−H OA (ΔG‡ = 10.7 kcal mol–1) is lower than that for C−Cl OA (ΔG‡ = 19.7 kcal mol–1). However, the C−Cl OA product is calculated to be thermodynamically preferred as its ΔGo is 14.3 kcal mol–1 below that for the most stable C−H OA product.

scholarly journals Molecular Mechanisms of Succinimide Formation from Aspartic Acid Residues Catalyzed by Two Water Molecules in the Aqueous Phase

2021 ◽  
Vol 22 (2) ◽  
pp. 509
Author(s):  
Tomoki Nakayoshi ◽  
Koichi Kato ◽  
Shuichi Fukuyoshi ◽  
Ohgi Takahashi ◽  
Eiji Kurimoto ◽  
...  
Keyword(s):  
Gas Phase ◽  
Aspartic Acid ◽  
Aqueous Phase ◽  
Molecular Mechanisms ◽  
Model Compound ◽  
Reaction Pathway ◽  
Single Point ◽  
Water Molecules ◽  
Age Related ◽  
Optimized Geometries

Aspartic acid (Asp) residues are prone to nonenzymatic isomerization via a succinimide (Suc) intermediate. The formation of isomerized Asp residues is considered to be associated with various age-related diseases, such as cataracts and Alzheimer’s disease. In the present paper, we describe the reaction pathway of Suc residue formation from Asp residues catalyzed by two water molecules using the B3LYP/6-31+G(d,p) level of theory. Single-point energies were calculated using the MP2/6-311+G(d,p) level of theory. For these calculations, we used a model compound in which an Asp residue was capped with acetyl and methylamino groups on the N- and C-termini, respectively. In the aqueous phase, Suc residue formation from an Asp residue was roughly divided into three steps, namely, iminolization, cyclization, and dehydration, with the activation energy estimated to be 109 kJ mol−1. Some optimized geometries and reaction modes in the aqueous phase were observed that differed from those in the gas phase.

Mechanisms for the formation of epoxide and chlorine-containing products in the oxidation of ethylene by chromyl chloride: a density functional study

1999 ◽  
Vol 77 (9) ◽  
pp. 1476-1491 ◽  
Author(s):  
Maricel Torrent ◽  
Liqun Deng ◽  
Miquel Duran ◽  
Miquel Solà ◽  
Tom Ziegler
Keyword(s):  
Density Functional Theory ◽  
Reaction Mechanisms ◽  
Density Functional ◽  
Activation Barrier ◽  
Activation Energies ◽  
Functional Study ◽  
Functional Theory ◽  
Activation Barriers ◽  
Density Functional Study ◽  
Chromyl Chloride

The reaction between CrO2Cl2 and ethylene leading to the formation of epoxide and chlorohydrin precursors or directly to 1,2-dichloroethane has been studied by density functional theory. The formation of the epoxide precursor (Cl2(O)Cr-OC2H4) was found to take place via a [3+2] addition of ethylene to two Cr=O bonds followed by rearrangement of the five-membered diol to the epoxide product. The alternative mechanisms involving a direct addition of oxygen to ethylene or the [2+2] addition of the olefin to a Cr=O bond were found to have much higher activation energies. The formation of the chlorohydrin precursor (Cl(O)Cr-OCH2=CHCl) was found to take place via a [3+2] addition to one Cr—Cl and one Cr=O bond. Pathways involving initial [2+2] addition to a Cr—Cl or Cr=O bond had much higher activation barriers. The generation of 1,2-dichloroethane is highly unfavorable with an endothermicity of 44.7 kcal/mol and an even higher activation barrier. It is suggested that the formation of epoxide and chlorohydrin from the respective precursors requires the addition of H2O.Key words: reaction mechanisms, epoxide, oxidation of ethylene, chromyl chloride, DFT.

scholarly journals Adsorption and Reaction Mechanisms of Direct Palladium Synthesis by ALD Using Pd(hfac)2 and Ozone on Si (100) Surface

Processes ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 2246
Author(s):  
Chunyu Cheng ◽  
Yiming Zou ◽  
Jiahui Li ◽  
Amanda Jiamin Ong ◽  
Ronn Goei ◽  
...  
Keyword(s):  
Reaction Mechanisms ◽  
Palladium Nanoparticles ◽  
Density Functional ◽  
Noble Metals ◽  
Activation Barrier ◽  
Atomic Layer ◽  
Activation Barriers ◽  
Layer Deposition ◽  
High Activation Barrier ◽  
Palladium Metal

Palladium nanoparticles made by atomic layer deposition (ALD) normally involve formaldehyde or H2 as a reducing agent. Since formaldehyde is toxic and H2 is explosive, it is advantageous to remove this reducing step during the fabrication of palladium metal by ALD. In this work we have successfully used Pd(hfac)2 and ozone directly to prepare palladium nanoparticles, without the use of reducing or annealing agents. Density functional theory (DFT) was employed to explore the reaction mechanisms of palladium metal formation in this process. DFT results show that Pd(hfac)2 dissociatively chemisorbed to form Pd(hfac)* and hfac* on the Si (100) surface. Subsequently, an O atom of the ozone could cleave the C–C bond of Pd(hfac)* to form Pd* with a low activation barrier of 0.46 eV. An O atom of the ozone could also be inserted into the hfac* to form Pd(hfac-O)* with a lower activation barrier of 0.29 eV. With more ozone, the C–C bond of Pd(hfac-O)* could be broken to produce Pd* with an activation barrier of 0.42 eV. The ozone could also chemisorb on the Pd atom of Pd(hfac-O)* to form O3-Pd(hfac-O)*, which could separate into O-Pd(hfac-O)* with a high activation barrier of 0.83 eV. Besides, the activation barrier was 0.64 eV for Pd* that was directly oxidized to PdOx by ozone. Based on activation barriers from DFT calculations, it was possible to prepare palladium without reducing steps when ALD conditions were carefully controlled, especially the ozone parameters, as shown by our experimental results. The mechanisms of this approach could be used to prepare other noble metals by ALD without reducing/annealing agents.

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