Mechanistic Insights into Protonated Diamines-catalyzed Decarboxylation of Oxaloacetate

2019 ◽  
Vol 16 (3) ◽  
pp. 202-208
Author(s):  
Chuangang Fan ◽  
Mingzhi Song
Keyword(s):  
Free Energy ◽  
Gibbs Free Energy ◽  
Density Functional ◽  
Catalytic Mechanism ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Chemical Mechanisms ◽  
Insight Into

The chemical mechanisms of protonated diamines-catalyzed decarboxylation of oxaloacetic acid anions in water solutions have been studied by using density functional theory. The calculated results show that the activated Gibbs free energy of the decarboxylation step is the highest in the whole diamine-catalytic processes for OA2-, and protonated ethylenediamine (ENH+) is the best catalyst of the five diamines, which is consistent with the study of Thalji et al. However, for OA-, different with OA2-, the dehydration step is the rate-determining one except 1,3-diaminopropane, and protonated 1,4- diaminobutane is the best catalyst of the five catalysts. The results also indicate that the second amino group participates in the reaction as the proton acceptor or proton donor, and it assists in decarboxylation by hydrogen bonds, decreasing the active Gibbs free energy barrier of the whole catalytic process. These results provide insight into the precise catalytic mechanism of several enzymes whose reactions are known to proceed via an imine intermediate.

scholarly journals Crystalline Peroxosolvates: Nature of the Coformer, Hydrogen-Bonded Networks and Clusters, Intermolecular Interactions

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 26
Author(s):  
Alexander G. Medvedev ◽  
Andrei V. Churakov ◽  
Petr V. Prikhodchenko ◽  
Ovadia Lev ◽  
Mikhail V. Vener
Keyword(s):  
Density Functional ◽  
High Energy ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Functional Theory ◽  
Sodium Percarbonate ◽  
Analgesic Effects ◽  
1D Chain ◽  
The Stability ◽  
Insight Into

Despite the technological importance of urea perhydrate (percarbamide) and sodium percarbonate, and the growing technological attention to solid forms of peroxide, fewer than 45 peroxosolvates were known by 2000. However, recent advances in X-ray diffractometers more than tripled the number of structurally characterized peroxosolvates over the last 20 years, and even more so, allowed energetic interpretation and gleaning deeper insight into peroxosolvate stability. To date, 134 crystalline peroxosolvates have been structurally resolved providing sufficient insight to justify a first review article on the subject. In the first chapter of the review, a comprehensive analysis of the structural databases is carried out revealing the nature of the co-former in crystalline peroxosolvates. In the majority of cases, the coformers can be classified into three groups: (1) salts of inorganic and carboxylic acids; (2) amino acids, peptides, and related zwitterions; and (3) molecular compounds with a lone electron pair on nitrogen and/or oxygen atoms. The second chapter of the review is devoted to H-bonding in peroxosolvates. The database search and energy statistics revealed the importance of intermolecular hydrogen bonds (H-bonds) which play a structure-directing role in the considered crystals. H2O2 always forms two H-bonds as a proton donor, the energy of which is higher than the energy of analogous H-bonds existing in isostructural crystalline hydrates. This phenomenon is due to the higher acidity of H2O2 compared to water and the conformational mobility of H2O2. The dihedral angle H-O-O-H varies from 20 to 180° in crystalline peroxosolvates. As a result, infinite H-bonded 1D chain clusters are formed, consisting of H2O2 molecules, H2O2 and water molecules, and H2O2 and halogen anions. H2O2 can form up to four H-bonds as a proton acceptor. The third chapter of the review is devoted to energetic computations and in particular density functional theory with periodic boundary conditions. The approaches are considered in detail, allowing one to obtain the H-bond energies in crystals. DFT computations provide deeper insight into the stability of peroxosolvates and explain why percarbamide and sodium percarbonate are stable to H2O2/H2O isomorphic transformations. The review ends with a description of the main modern trends in the synthesis of crystalline peroxosolvates, in particular, the production of peroxosolvates of high-energy compounds and mixed pharmaceutical forms with antiseptic and analgesic effects.

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 First-Principles Study of Mechanical and Thermodynamic Properties of Binary and Ternary CoX (X = W and Mo) Intermetallic Compounds

Materials ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1404
Author(s):  
Yunfei Yang ◽  
Changhao Wang ◽  
Junhao Sun ◽  
Shilei Li ◽  
Wei Liu ◽  
...  
Keyword(s):  
Free Energy ◽  
Thermodynamic Properties ◽  
Gibbs Free Energy ◽  
Density Functional ◽  
Vibrational Entropy ◽  
Functional Theory ◽  
Lattice Constants ◽  
The Density Functional Theory ◽  
Ductile Behavior ◽  
Pseudo Potential

In this study, the structural, elastic, and thermodynamic properties of DO19 and L12 structured Co3X (X = W, Mo or both W and Mo) and μ structured Co7X6 were investigated using the density functional theory implemented in the pseudo-potential plane wave. The obtained lattice constants were observed to be in good agreement with the available experimental data. With respect to the calculated mechanical properties and Poisson’s ratio, the DO19-Co3X, L12-Co3X, and μ-Co7X6 compounds were noted to be mechanically stable and possessed an optimal ductile behavior; however, L12-Co3X exhibited higher strength and brittleness than DO19-Co3X. Moreover, the quasi-harmonic Debye–Grüneisen approach was confirmed to be valid in describing the temperature-dependent thermodynamic properties of the Co3X and Co7X6 compounds, including heat capacity, vibrational entropy, and Gibbs free energy. Based on the calculated Gibbs free energy of DO19-Co3X and L12-Co7X6, the phase transformation temperatures for DO19-Co3X to L12-Co7X6 were determined and obtained values were noted to match well with the experiment results.

scholarly journals A density functional theory study of the oxygen reduction reaction on the (111) and (100) surfaces of cobalt(II) oxide

2019 ◽  
Vol 44 (2) ◽  
pp. 122-131
Author(s):  
Bangchang Qin ◽  
Yang Tian ◽  
Pengxiang Zhang ◽  
Zuoyin Yang ◽  
Guoxin Zhang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Free Energy ◽  
Oxygen Reduction Reaction ◽  
Oxygen Reduction ◽  
Gibbs Free Energy ◽  
Density Functional ◽  
Rational Design ◽  
Reduction Reaction ◽  
Functional Theory ◽  
Associative Mechanism

Density functional theory calculations were employed to investigate the electrochemical oxygen reduction reaction on the (111) and (100) surfaces of cobalt(II) oxide. Different mechanisms were applied to evaluate the oxygen reduction reaction performance of cobalt(II) oxide structures in terms of the Gibbs free energy and density of states. A variety of intermediate structures based on associative and dissociative mechanisms were constructed and optimized. As a result, we estimated the catalytic activity by calculating the free energy of the intermediates and constructing free energy diagrams, which suggested that the oxygen reduction reaction Gibbs free energy on cobalt(II) oxide (111) and (100) surfaces based on the associative mechanism is smaller than that based on the dissociative mechanism, demonstrating that the associative mechanism should be more likely to be the oxygen reduction reaction pathway. Moreover, the theoretical oxygen reduction reaction activity on the cobalt(II) oxide (111) surface was found to be higher than that on the cobalt(II) oxide (100) surface. These results shed light on the rational design of high-performance cobalt(II) oxide oxygen reduction reaction catalysts.

scholarly journals New Rod-Like H-Bonded Assembly Systems: Mesomorphic and Geometrical Aspects

Crystals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 795
Author(s):  
Laila A. Al-Mutabagani ◽  
Latifah Abdullah Alshabanah ◽  
Hoda A. Ahmed ◽  
Khulood A. Abu Al-Ola ◽  
Mohamed Hagar
Keyword(s):  
Density Functional ◽  
Polarized Light ◽  
Proton Donor ◽  
Proton Acceptor ◽  
Scanning Calorimetry ◽  
Functional Theory ◽  
Ft Ir ◽  
Ir Spectroscopic ◽  
Thermal Stability Of ◽  
Bonded Complexes

Experimental and geometrical approaches of new systems of mesomorphic 1:1 supramolecular H-bonded complexes (SMHBCs) of five rings are discussed. The H-bonding between 4-alkoxyphenylimino benzoic acids (An, as proton acceptor) and 4-(4′–pyridylazophenyl) 4′′-alkoxybenzoates (Bm, as proton donor) were investigated. Mesomorphic behaviors were analyzed by differential scanning calorimetry (DSC) and mesophase textures were identified by polarized light microscopy (POM). H-bonded assembly was established by FT-IR spectroscopic measurements via Fermi band discussion. Thermal and theoretical factors were predicted for all synthesized complexes by density functional theory (DFT) predictions. The results revealed that all prepared complexes were monomorphic, with a broad range of smectic A phases with a high thermal stability of enantiotropic mesophase. Furthermore, DFT stimulations illustrated the experimental results in terms of the influence of the chain length either of the acid or the base component. Many parameters, such as the calculated stability, the dipole moment and the polarizability of the H-bonded complexes, illustrate how these parameters work together to enhance the smectic mesophases with the obtained stability and range.

scholarly journals Bioinspired Design and Computational Prediction of SCS Nickel Pincer Complexes for Hydrogenation of Carbon Dioxide

Catalysts ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 319
Author(s):  
Xiaoyun Liu ◽  
Bing Qiu ◽  
Xinzheng Yang
Keyword(s):  
Free Energy ◽  
Formic Acid ◽  
Functional Groups ◽  
Density Functional ◽  
Catalytic Mechanism ◽  
Activation Mechanism ◽  
Free Energy Barrier ◽  
Energy Barriers ◽  
Hydrogenation Of Co2 ◽  
Model Complex

Inspired by the structures of the active site of lactate racemase and H2 activation mechanism of mono-iron hydrogenase, we proposed a series of sulphur–carbon–sulphur (SCS) nickel complexes and computationally predicted their potentials for catalytic hydrogenation of CO2. Density functional theory calculations reveal a metal–ligand cooperated mechanism with the participation of a sulfur atom in the SCS pincer ligand as a proton receiver for the heterolytic cleavage of H2. For all newly proposed complexes containing functional groups with different electron-donating and withdrawing abilities in the SCS ligand, the predicted free energy barriers for the hydrogenation of CO2 to formic acid are in a range of 22.2–25.5 kcal/mol in water. Such a small difference in energy barriers indicates limited contributions of those functional groups to the charge density of the metal center. We further explored the catalytic mechanism of the simplest model complex for hydrogenation of formic acid to formaldehyde and obtained a total free energy barrier of 34.6 kcal/mol for the hydrogenation of CO2 to methanol.

Mechanistic Study of the Cooperative Palladium/Lewis Acid-Catalyzed Transfer Hydrocyanation Reaction: The Origin of the Regioselectivity

2021 ◽  
Author(s):  
Dandan Jiang ◽  
Xiaojun Li ◽  
Jiali Cai ◽  
Yuna Bai ◽  
Lixiong Zhang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Dft Calculations ◽  
Lewis Acid ◽  
Density Functional ◽  
Catalytic Mechanism ◽  
Mechanistic Study ◽  
Functional Theory ◽  
Terminal Alkenes ◽  
Acid Catalyzed ◽  
Insight Into

Density functional theory (DFT) calculations have been performed to gain insight into the catalytic mechanism of the Palladium/Lewis acid-catalyzed transfer hydrocyanation of terminal alkenes to reach the linear alkyl nitrile...

Relaxed structure of typical nitro explosives in the excited state: observation and implication

2017 ◽  
Author(s):  
Genbai Chu
Keyword(s):  
Excited State ◽  
Excitation Energy ◽  
Nitro Group ◽  
Density Functional ◽  
Functional Theory ◽  
Chemical Mechanisms ◽  
State Observation ◽  
Nitro Explosives ◽  
Physical And Chemical ◽  
Insight Into

<a></a><a></a><a></a><a>U</a><a></a><a></a><a></a><a></a><a></a><a>nderstanding the structural, geometrical and chemical changes that occur after electronic excitation is essential to unraveling the inherent physical and chemical mechanisms of nitro explosives. In this work, the relaxed structure of some typical nitro explosives in the excited state, including RDX, HMX, CL-20, PETN and LLM-105, have been investigated by time-dependent density functional theory. During the excitation process, an electron is vertically excited into a low-lying excited state, imparting π-antibonding character onto the nitro group. The nitro group becomes activated by the excitation energy and then relaxes via vibrational cooling, leading to a relaxed excited-state structure. </a><a></a><a>All five nitro explosives exhibit similar behavior in which impact sensitivity is related to the excitation energy of the relaxed structure.</a> <a></a><a>Insight into the relaxed structure of typical nitro explosives offers an efficient method of unraveling ultrafast and complex photo-initiated reactions and detonation physics</a>.

Relaxed structure of typical nitro explosives in the excited state: observation and implication

2017 ◽  
Author(s):  
Genbai Chu
Keyword(s):  
Excited State ◽  
Excitation Energy ◽  
Nitro Group ◽  
Density Functional ◽  
Functional Theory ◽  
Chemical Mechanisms ◽  
State Observation ◽  
Nitro Explosives ◽  
Physical And Chemical ◽  
Insight Into

<a></a><a></a><a></a><a>U</a><a></a><a></a><a></a><a></a><a></a><a>nderstanding the structural, geometrical and chemical changes that occur after electronic excitation is essential to unraveling the inherent physical and chemical mechanisms of nitro explosives. In this work, the relaxed structure of some typical nitro explosives in the excited state, including RDX, HMX, CL-20, PETN and LLM-105, have been investigated by time-dependent density functional theory. During the excitation process, an electron is vertically excited into a low-lying excited state, imparting π-antibonding character onto the nitro group. The nitro group becomes activated by the excitation energy and then relaxes via vibrational cooling, leading to a relaxed excited-state structure. </a><a></a><a>All five nitro explosives exhibit similar behavior in which impact sensitivity is related to the excitation energy of the relaxed structure.</a> <a></a><a>Insight into the relaxed structure of typical nitro explosives offers an efficient method of unraveling ultrafast and complex photo-initiated reactions and detonation physics</a>.

High Throughput Virtual Screening of 200 Billion Molecular Solar Heat Battery Candidates

2019 ◽  
Author(s):  
Mads Koerstz ◽  
Anders S. Christensen ◽  
Kurt V. Mikkelsen ◽  
Mogens Brøndsted Nielsen ◽  
Jan H. Jensen
Keyword(s):  
Free Energy ◽  
Density Functional ◽  
Parent Compound ◽  
High Energy ◽  
Back Reaction ◽  
Free Energy Barrier ◽  
Promising Candidate ◽  
Functional Theory ◽  
Practical Applications ◽  
Quantum Chemical Methods

<div>The dihydroazulene/vinylheptafulvene (DHA/VHF) thermocouple is a promising candidate for thermal heat batteries that absorb and store solar energy as chemical energy without the need for insulation. However, in order to be viable the energy storage capacity and stability of the high energy form (the free energy barrier to the back reaction) must be increased significantly. We use semiempirical quantum chemical methods, machine learning, genetic algorithms, and density functional theory to virtually screen roughly 200 billion substituted DHA molecules to identify promising candidates for further study. We identify three molecules with predicted energy densities of (0.34-0.36 kJ/g), which is significantly larger than the 0.14 kJ/g computed for the parent system. The free energy barriers to the back reaction are between 6.8 and 7.7 kJ/mol higher than the parent compound, which should correspond to half-lives of days - sufficiently long for many practical applications.</div>

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