scholarly journals Effect of the Nucleophile’s Nature on Chloroacetanilide Herbicides Cleavage Reaction Mechanism. A DFT Study

2021 ◽  
Vol 22 (13) ◽  
pp. 6876
Author(s):  
Sebastián A. Cuesta ◽  
F. Javier Torres ◽  
Luis Rincón ◽  
José Luis Paz ◽  
Edgar A. Márquez ◽  
...  
Keyword(s):  
Activation Energy ◽  
Transition State ◽  
Chemical Potential ◽  
Degradation Mechanism ◽  
Nbo Analysis ◽  
Basis Set ◽  
Nucleophilic Attack ◽  
Hybrid Functional ◽  
Chloroacetanilide Herbicides ◽  
Late Transition

In this study, the degradation mechanism of chloroacetanilide herbicides in the presence of four different nucleophiles, namely: Br−, I−, HS−, and S2O3−2, was theoretically evaluated using the dispersion-corrected hybrid functional wB97XD and the DGDZVP as a basis set. The comparison of computed activation energies with experimental data shows an excellent correlation (R2 = 0.98 for alachlor and 0.97 for propachlor). The results suggest that the best nucleophiles are those where a sulfur atom performs the nucleophilic attack, whereas the other species are less reactive. Furthermore, it was observed that the different R groups of chloroacetanilide herbicides have a negligible effect on the activation energy of the process. Further insights into the mechanism show that geometrical changes and electronic rearrangements contribute 60% and 40% of the activation energy, respectively. A deeper analysis of the reaction coordinate was conducted, employing the evolution chemical potential, hardness, and electrophilicity index, as well as the electronic flux. The charge analysis shows that the electron density of chlorine increases as the nucleophilic attack occurs. Finally, NBO analysis indicates that the nucleophilic substitution in chloroacetanilides is an asynchronous process with a late transition state for all models except for the case of the iodide attack, which occurs through an early transition state in the reaction.

scholarly journals Study on the chemical potential of apigenin, luteolin, quercetin, and myricetin using the molecular modeling

2021 ◽  
Vol 44 (1) ◽  
pp. 63-66
Author(s):  
Steluta Gosav ◽  
Adriana Hodorogea ◽  
Dan Maftei
Keyword(s):  
Gas Phase ◽  
Chemical Potential ◽  
Chemical Compounds ◽  
Molecular Structures ◽  
Basis Set ◽  
Chemical Hardness ◽  
Equilibrium Geometry ◽  
Hybrid Functional ◽  
Electrophilicity Index ◽  
Quantum Molecular Descriptors

In the present paper, the chemical potential of four flavonoids i.e. apigenin, luteolin, quercetin, and myricetin, of interest in the pharmaceutical industry was investigated using molecular modelling. The equilibrium geometry of molecular structures was calculated in the gas phase and ground state by using B3LYP hybrid functional in conjunction with a 6-311G(d,p) basis set. In order to assess the chemical potential of investigated flavonoids, the main quantum molecular descriptors, such as the dipole moment, the energy of the highest/lowest occupied/unoccupied molecular orbital, the gap energy, the electronegativity, the chemical hardness/softness, and the electrophilicity index have been computed. Also, the influence of the hydroxylation degree of chemical compounds on the chemical potential is discussed.

scholarly journals Prototropic and metallotropic migration of isolobal fragments on indol rings. Theoretical study and NBO analysis

2009 ◽  
Vol 5 (1) ◽  
pp. 614-625
Author(s):  
Saeed Jameh-Bozorghi ◽  
Zahra Javanshir ◽  
D. Nori Shargh
Keyword(s):  
Activation Energy ◽  
Ambient Temperature ◽  
Ab Initio ◽  
Theoretical Study ◽  
Nbo Analysis ◽  
Molecular Structures ◽  
Basis Set ◽  
Lower Amount ◽  
Temperature Calculation ◽  
Calculation Results

Molecular structures, energies, NBO analysis and sigmatropic behaviour of 1-Indenyl(dihydro)borane (1) and 1-Indenyl-threecarbonylcobalt(I) (2) were investigated using DFT and ab initio molecular orbital methods. In these compounds BH2 and Co(CO)3 fragments areisolobal. The Results of calculations using B3LYP, HF and MP2methods [Basis set 6-311+G**] showed that -BH2 and -Co(CO)3 had similar behaviour in sigmatropic shifts. Prototropic shifts in compounds 1 and 2 have similar mechanisms too. Results showed that metallotrotropic shift is faster than Prototrpic shift in compounds 1 and 2. The activation energies (Ea) of Prototropic shift in compounds 1 and 2 are 18.83 and 17.38 kcal.mol-1. These energies are higher than -BH2 shifts in compound 1 (10.11 kcal.mol-1) or migration of -Co(CO)3 fragment in compound 2 (12.39 kcal.mol-1). Lower amount of activation energy in borotropic shift and cobalt`s fragment shift show that rotation of boron and cobalt on the indol ring can happen in the ambient temperature. Calculation results revealed that migration of proton and Co(CO)3 was carried out via suprafacial[1,2]-sigmatropic mechanism while -BH2 shift took place via antrafacial [1,3]-rearangment. 

A DFT investigation of axial N-donor ligands effects on the high valent manganese-oxo meso-tetraphenyl porphyrin

2015 ◽  
Vol 19 (05) ◽  
pp. 651-662 ◽  
Author(s):  
Hossein Kavousi ◽  
Abdolreza Rezaeifard ◽  
Heidar Raissi ◽  
Maasoumeh Jafarpour
Keyword(s):  
Density Functional ◽  
Chemical Potential ◽  
Water Solution ◽  
Nbo Analysis ◽  
Basis Set ◽  
Donor Ligands ◽  
Chemical Hardness ◽  
B3lyp Method ◽  
Nitrogen Donors ◽  
High Valent

The effect of different electronic and structural nitrogen donors (L) on the N ( ax )- Mn - O properties in the high valent manganese-oxo meso-tetraphenylporphyrin intermediate is investigated by the density functional B3LYP method with 6-31g* basis set. The geometric structures, frontier molecular orbitals, thermodynamic parameters and physical properties such as chemical potential and chemical hardness of [( TPP )( L ) MnO ]+ complexes in the gas phase as well as water solution are calculated. Our theoretical results confirm that the Mn - O distances in [( TPP )( L ) MnO ]+ species decrease by replacing imidazoles with pyridines, amins as well as electron-poor and hindered nitrogen donors resulting from extending the Mn – N ( ax ) bonds. These results are supported by vibrational frequencies, atoms in molecules (AIM) and natural bond orbital (NBO) analysis. It is worth mentioning that the co-catalytic activity trend of different nitrogen donors observed experimentally in the presence of title Mn porphyrin is consistent with the calculated Mn – N ( ax ) and Mn – O bond lengths in this work.

SN2 reactions in the gas phase. Transition states for the reaction: Cl− + RBr = ClR + Br−, where R = CH3, C2H5, and iso-C3H7, from abinitio calculations and comparison with experiment. Solvent effects

1989 ◽  
Vol 67 (8) ◽  
pp. 1262-1267 ◽  
Author(s):  
Kimihiko Hirao ◽  
Paul Kebarle
Keyword(s):  
Experimental Data ◽  
Activation Energy ◽  
Aqueous Solution ◽  
Transition State ◽  
Gas Phase ◽  
Closed Shell ◽  
Basis Set ◽  
Phase Reaction ◽  
Ion Molecule Reactions ◽  
Abinitio Calculations

The geometries and the energies of the reactants, transition state, and products for the gas phase reaction: Cl− + CH3Br = ClCH3 + Br−, were obtained from abinitio calculations using a closed shell SCF method with a MINI basis set developed by Huzinaga etal. The energy changes predicted by the calculations are found in good agreement with the experimental data. The energies and geometries of the reactants and the transition state for the gas phase reactions: Cl− + RBr = ClR + Br−, where R = C2H5 and iso-C3H7, were also obtained. The resulting activation energies follow the same trend as the experimental data: Me < Et < iso-Pr; however, the predicted increase of activation energy is considerably larger. The energies and geometries for the reactants, transition state, and products of the gas phase ion-dihydrate reaction: Cl−(H2O)2 + CH3Br → H2O(ClCH3Br)−H2O → Br−(H2O)2 + CH3Cl were obtained as well. These data provide an interesting comparison with experimental results in aqueous solution. The reaction coordinate of the ion-dihydrate reaction is very much closer to that for aqueous solution than to that for the gas phase. Keywords: nucleophilic substitution reactions, ion–molecule reactions, activation energy.

Stereoelectronic effects of porphyrin ligand on the oxygen transfer efficiency of high valent manganese-oxo porphyrin species: A DFT study

2015 ◽  
Vol 19 (10) ◽  
pp. 1130-1139 ◽  
Author(s):  
Hossein Kavousi ◽  
Heidar Raissi ◽  
Abdolreza Rezaeifard ◽  
Maasoumeh Jafarpour
Keyword(s):  
Density Functional ◽  
Chemical Potential ◽  
Water Solution ◽  
Dft Method ◽  
Nbo Analysis ◽  
Basis Set ◽  
Chemical Hardness ◽  
Third Generation ◽  
Oxygen Transfer Efficiency ◽  
High Valent

The structure and properties of the N[Formula: see text]–Mn–O bonds of high valent manganese-oxo of the second and third generation porphyrins in the presence of imidazole have been studied by means of density functional (DFT) method with 6-31G* basis set in the gas phase as well as water solution. The geometric structures, frontier molecular orbitals, thermodynamic parameters, aromaticity indices and physical properties such as chemical potential and chemical hardness of [(TPP)(ImH)MnO][Formula: see text] and its derivatives were calculated. The obtained results showed that [(TPP)(ImH)MnO][Formula: see text] bearing halogen atoms at the [Formula: see text]-pyrrole positions had a saddle conformation with low Mn–O strength. The electron density ([Formula: see text] and Laplacian ([Formula: see text] properties at critical points of the N[Formula: see text]–Mn–O bonds, estimated by AIM calculations, indicate that Mn–O bonds in third generation porphyrins have lower [Formula: see text] and Mn–N[Formula: see text] distances have higher [Formula: see text] than the second generation ones. The calculations of aromaticity indices for chelated rings at the porphyrin center show that HOMA and NICS in third generation porphyrins are generally lower than that of second ones which is in agreement with their saddle conformation. These results are supported by natural bond orbital (NBO) analysis.

scholarly journals Comparative study of molecular docking, structural, electronic, vibrational and hydrogen bonding interactions on 4-hydroxy benzo hydrazide (4HBH) and its newly designed derivative [(E)–N′-((1H-Pyrrol-2-YL)methylene) –4-hydroxy benzo hydrazide and its isomers (I, II and III)] (potential inhibitors) for COVID-19 protease

2021 ◽  
pp. 1-21
Author(s):  
Anoop Kumar Pandey ◽  
Vijay Singh ◽  
Apoorva Dwivedi
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Basis Set ◽  
Hybrid Functional ◽  
Linear Optical Properties ◽  
Vibrational Bands ◽  
The One ◽  
Potential Inhibitors

Studies have shown that hydrazides and thier derivatives are used for pharmaceutical and medicinal purposes. At present, the whole world is suffering for COVID-19 virus. There are some vaccines or medicines available to treat this disease all over the world. Today the one fourth of the world’s population is under lockdown condition. In this scenario, scientists from the whole world are doing different types of research on this disease. Being a molecular modeller, this inspires us to design new types of species (may be drugs) which may be capable for COVID-19 Protease. In the present effort, we have performed docking studies of title compounds with COVID-19 protein (6LU7) for anti-COVID-19 activity. A comparative quantum chemical calculations of molecular geometries (bond lengths and bond angles) of 4-Hydroxy Benzo Hydrazide (4HBH) and its newly designed derivatve [(E)-N′-((1H-Pyrrol-2-YL)Methylene) –4-Hydroxy Benzo Hydrazide and its isomers (I, II and III)] in the ground state have also been carried out due to its biological importance and compared with the similer type of compound found in literature i.e. benzohydrazide. The optimized geometry and wavenumber of the vibrational bands of the molecules have been calculated by density functional theory (DFT) using Becke’s three-parameters hybrid functional (B3LYP/CAM-B3LYP) with 6–311G (d, p) as the basis set. Vibrational wavenumbers are compared with the observed FT-IR and FTRaman spectra of 4-Hydroxy Benzo Hydrazide. TDDFT calculations are also done on the same level of theory and a theoretical UV-vis spectrum of title molecules are also drawn. HOMO-LUMO analysis has been done to describe the way the molecule interacts with other species. Natural bond orbitals (NBO) analysis has been carried out to inspect the intra- and inter- molecular hydrogen-bonding, conjugative and hyper conjugative interactions and their second order stabilization energy. Nonlinear optical (NLO) analysis has been performed to study the non-linear optical properties of the molecule by computing the first hyperpolarizability. The variation of thermodynamic properties with temperature has been studied. QATIM analysis shows that hydrogen bonding occurs in 4HBH, isomer II and III respectively.

Density functional theory, Comparative vibrational spectroscopic studies, HOMO-LUMO, and NBO analysis of Trichloro isocyanuric acid and Trithio cyanuric acid

2015 ◽  
Vol 8 (3) ◽  
pp. 2197-2221
Author(s):  
Theraviyum Chithambarathanu ◽  
M. Darathi ◽  
J. DaisyMagdaline ◽  
S. Gunasekaran
Keyword(s):  
Density Functional ◽  
Cyanuric Acid ◽  
Nbo Analysis ◽  
Basis Set ◽  
Potential Energy Distribution ◽  
Point Energy ◽  
Isocyanuric Acid ◽  
Ft Ir ◽  
Homo Lumo ◽  
Ft Raman

The molecular vibrations of Trichloro isocyanuric acid (C3Cl3N3O3) and Trithio cyanuric acid (C3H3N3S3) have been investigated in polycrystalline sample at room temperature by Fourier Transform Infrared (FT-IR) and FT-Raman spectroscopies in the region 4000-450 cm-1 and 4000-50 cm-1 respectively, which provide a wealth of structural information about the molecules. The spectra are interpreted with the aid of normal co-ordinate analysis following full structure optimization and force field calculations based on density functional theory   (DFT) using standard B3LYP / 6-311++ G (d, p) basis set for investigating the structural and spectroscopic properties. The vibrational frequencies are calculated and the scaled values are compared with experimental FT-IR and FT-Raman spectra. The scaled theoretical wave numbers shows very good agreement with experimental ones. The complete vibrational assignments are performed on the basis of potential energy distribution (PED) of vibrational modes, calculated with scaled quantum (SQM) method. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that change in electron density (ED) in σ* and π* anti-bonding orbitals and second order delocalization   energy (E2) confirm the occurrence of Intra molecular Charge Transfer (ICT) within the molecule. The thermodynamic properties like heat capacity, entropy, enthalpy and zero point energy have been calculated for the molecule. The frontier molecular orbitals have been visualized and the HOMO-LUMO energy gap has been calculated. The Molecular Electrostatic Potential (MEP) analysis reveals the sites for electrophilic attack and nucleophilic reactions in the molecule.

Quantum Mechanical Investigation of Geometrical Structure and Dynamic Behavior of h-BNNT (9,9-5) and h-AlNNT (9,9-5)Single-Walled Nanotubes: NBO Analysis

2019 ◽  
Vol 16 (9) ◽  
pp. 705-717
Author(s):  
Mehrnoosh Khaleghian ◽  
Fatemeh Azarakhshi
Keyword(s):  
Carbon Nanotubes ◽  
Density Functional ◽  
Structural Parameters ◽  
Energy Levels ◽  
Nbo Analysis ◽  
Electronic Energy ◽  
Boron Nitride Nanotubes ◽  
Basis Set ◽  
B3lyp Method ◽  
Mechanical Investigation

In the present research, B45H36N45 Born Nitride (9,9) nanotube (BNNT) and Al45H36N45 Aluminum nitride (9,9) nanotube (AlNNT) have been studied, both having the same length of 5 angstroms. The main reason for choosing boron nitride nanotubes is their interesting properties compared with carbon nanotubes. For example, resistance to oxidation at high temperatures, chemical and thermal stability higher rather than carbon nanotubes and conductivity in these nanotubes, unlike carbon nanotubes, does not depend on the type of nanotube chirality. The method used in this study is the density functional theory (DFT) at Becke3, Lee-Yang-Parr (B3LYP) method and 6-31G* basis set for all the calculations. At first, the samples were simulated and then the optimized structure was obtained using Gaussian 09 software. The structural parameters of each nanotube were determined in 5 layers. Frequency calculations in order to extract the thermodynamic parameters and natural bond orbital (NBO) calculations have been performed to evaluate the electron density and electrostatic environment of different layers, energy levels and related parameters, such as ionization energy and electronic energy, bond gap energy and the share of hybrid orbitals of different layers.

Microscopic Interpretation of Arrhenius Parameters

2018 ◽  
Author(s):  
Niels Engholm Henriksen ◽  
Flemming Yssing Hansen
Keyword(s):  
Activation Energy ◽  
Transition State ◽  
Transition State Theory ◽  
Average Energy ◽  
Zero Point ◽  
State Theory ◽  
Exponential Factor ◽  
Quantum Tunnelling ◽  
Microscopic Interpretation ◽  
The Difference

This chapter reviews the microscopic interpretation of the pre-exponential factor and the activation energy in rate constant expressions of the Arrhenius form. The pre-exponential factor of apparent unimolecular reactions is, roughly, expected to be of the order of a vibrational frequency, whereas the pre-exponential factor of bimolecular reactions, roughly, is related to the number of collisions per unit time and per unit volume. The activation energy of an elementary reaction can be interpreted as the average energy of the molecules that react minus the average energy of the reactants. Specializing to conventional transition-state theory, the activation energy is related to the classical barrier height of the potential energy surface plus the difference in zero-point energies and average internal energies between the activated complex and the reactants. When quantum tunnelling is included in transition-state theory, the activation energy is reduced, compared to the interpretation given in conventional transition-state theory.

On the use of Ozawa/Flynn/Wall method to determine aging activation energy for elastomers

2021 ◽  
pp. 009524432110203
Author(s):  
Sudhir Bafna
Keyword(s):  
Mechanical Properties ◽  
Activation Energy ◽  
Weight Loss ◽  
Oxygen Consumption ◽  
Dwell Time ◽  
Room Temperature ◽  
Elevated Temperatures ◽  
Degradation Mechanism ◽  
Kinetics Of ◽  
Wall Method

It is often necessary to assess the effect of aging at room temperature over years/decades for hardware containing elastomeric components such as oring seals or shock isolators. In order to determine this effect, accelerated oven aging at elevated temperatures is pursued. When doing so, it is vital that the degradation mechanism still be representative of that prevalent at room temperature. This places an upper limit on the elevated oven temperature, which in turn, increases the dwell time in the oven. As a result, the oven dwell time can run into months, if not years, something that is not realistically feasible due to resource/schedule constraints in industry. Measuring activation energy (Ea) of elastomer aging by test methods such as tensile strength or elongation, compression set, modulus, oxygen consumption, etc. is expensive and time consuming. Use of kinetics of weight loss by ThermoGravimetric Analysis (TGA) using the Ozawa/Flynn/Wall method per ASTM E1641 is an attractive option (especially due to the availability of commercial instrumentation with software to make the required measurements and calculations) and is widely used. There is no fundamental scientific reason why the kinetics of weight loss at elevated temperatures should correlate to the kinetics of loss of mechanical properties over years/decades at room temperature. Ea obtained by high temperature weight loss is almost always significantly higher than that obtained by measurements of mechanical properties or oxygen consumption over extended periods at much lower temperatures. In this paper, data on five different elastomer types (butyl, nitrile, EPDM, polychloroprene and fluorocarbon) are presented to prove that point. Thus, use of Ea determined by weight loss by TGA tends to give unrealistically high values, which in turn, will lead to incorrectly high predictions of storage life at room temperature.

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