B3LYP Level Of Theory Research Articles

Synthesis, crystal structure, DFT studies and evaluation of the antioxidant activity of 3,4-dimethoxybenzenamine schiff bases.

Schiff bases of 3,4-dimethoxybenzenamine 1–25 were synthesized and evaluated for their antioxidant activity. All the synthesized compounds were characterized by various spectroscopic techniques. In addition, the characterizations of compounds 13, 15 and 16 were supported by crystal X-ray determinations and their geometrical parameters were compared with theoretical DFT calculations at the B3LYP level of theory. Furthermore, the X-ray crystal data of two non-crystalline compounds 8 and 18 were theoretically calculated and compared with the practical values of compounds 13, 15, 16 and found a good agreement. The compounds showed good DPPH scavenging activity ranging from 10.12 to 84.34 μM where compounds 1–4 and 6 showed stronger activity than the standard n-propyl gallate. For the superoxide anion radical assay, compounds 1–3 showed better activity than the standard.

Theoretical study on the isomerization and tautomerism in barbituric acid

Isomerization and tautomerism of 16 isomers of barbituric acid (BA) were studied at the MP2 and B3LYP levels of theory. Activation energies (Ea), imaginary frequencies (υ), and Gibbs free energies (ΔG#) of the amine-imine and keto-enol tautomerisms and O–H internal rotations were calculated. The activation energies of amine-imine tautomerisms were in the range of 110–200 kJ/mol and for keto-enol tautomerisms were larger than 200 kJ/mol. The calculated activation energies of internal O–H rotations were smaller than 60 kJ/mol. Effect of micro-hydration on the transition state structures and activation energies of the tautomerisms were also investigated. Water molecule catalyzed the tautomerisms and decreased the activation energies of both the amine-imine and keto-enol tautomerisms about 100–120 kJ/mol.

A mechanistic study of fragmentation of deprotonated N,2-diphenyl-acetamides in electrospray ionization tandem mass spectrometry.

Exploring the fragmentation mechanism of amide ions in mass spectrometry has attracted great interest because of the desire to analyze the amino acid sequences of peptides and proteins. However, the collision-induced dissociation (CID) mechanism of deprotonated small amides has been rarely studied in electrospray ionization mass spectrometry (ESI-MS). The fragmentation of deprotonated N,2-diphenylacetamides exhibited some characteristic fragment ions, which are not derived from the conventional cleavage route. Therefore, clarification of their fragmentation mechanism is very important and useful for structural analysis of related amides and peptides. All CID experiments were carried out using an electrospray ionization ion trap mass spectrometer in negative ion mode. In addition, the accurate masses of fragments were measured on an ESI quadrupole time-of-flight (Q-TOF) mass spectrometer in negative ion mode. Deuterium-labeled 2-phenyl-N-(4-trifluoromethylphenyl)acetamide was synthesized and its ESI fragmentation spectrum had been obtained. Theoretical calculations were carried out by the density functional theory (DFT) method at the B3LYP level of theory with the 6-31G++(d,p) basis set. Deprotonated N,2-diphenylacetamides mainly generate four kinds of ions in CID: benzyl anion, aniline anion, phenyl-ethenone anion and isocyanato-benzene anion bearing respective substituent groups. The benzyl anion and the aniline anion can be generated by direct decomposition. The phenyl-ethenone anion and the isocyanato-benzene anion were proposed to be yielded from proton transfer within an ion-neutral complex, and the intensities of two competitive product ions are well correlated with the substituent constants. The mechanism was also supported by theoretical calculations. The characteristic fragment ions of deprotonated N,2-diphenylacetamides were proposed to be produced via an ion-neutral complex mechanism, which was proved by deuterium-labeling experiments, theoretical calculations and substituent effects.

Intramolecular H-transfer in CH2OO and cis-HO3

Intramolecular H-transfer reactions in cis-HO3 and CH2OO were studied at the MP2 and B3LYP levels of theory. Activation energies (E a) and Gibbs free energies of activation (∆G #) of the H-transfer reactions were calculated. The activation energies of the H-transfer in cis-HO3 and CH2OO were about 110 and 130 kJ/mol, respectively. Catalytic effects of some protic molecules including HCOOH, CH3OH, NH3, CH3NH2, HOCl, H2O2, and H2O, on the activation energies and transition state structures were studied. The more stable transition state structures were obtained in the presence of the protic molecules. Our calculations showed that the protic molecules decrease the activation energies of the H-transfer reactions about 50 kJ/mol.

Adsorption and dissociation of nitrous oxide on pristine and defective BeO and ZnO nanotubes: DFT studies

Adsorption of N2O on pristine and oxygen vacancy defect ZnO and BeO nanotubes was studied at the B3LYP and M06-2X levels of theory. It was found that this molecule can be used to repair the oxygen vacancy defects of these tubes. Adsorption energies of the dissociation of N2O on the defective BeO and ZnO nanotubes were calculated to be about 786.2 and 506.1 kJ/mol at the B3LYP level of theory, respectively. Molecular adsorption is barrierless, while the dissociative adsorptions have to overcome a small activation energy.

Structural and energetic characterization of the tautomers 2-benzothiazolinone and 2-hydroxybenzothiazole

This work reports an experimental and computational thermochemical study for 2-benzothiazolinone. The standard (p°=0.1MPa) molar energy of combustion of this compound was measured by rotating bomb combustion calorimetry. The standard molar enthalpy of the corresponding transition from crystalline to gaseous phases, at T=298.15K, was obtained from high temperature Calvet microcalorimetry measurements. The experimental results enable the calculation of the standard molar enthalpy of formation of the compound, in the gaseous state, at T=298.15K.The gas-phase enthalpies of formation of the title compounds, 2-benzothiazolinone and its enol form 2-hydroxybenzothiazole, were estimated computationally from high-level ab initio molecular orbital calculations at the G3(MP2)//B3LYP level of theory. The computed value for the keto form compares very well with the experimental result obtained in this work. The hydroxy↔oxo tautomerism of the title compounds was explored in this work as it may be relevant to their ability to occur as different polymorphic forms.

Quantum chemical study of atmospheric aggregates: HCl•HNO3•H2SO4.

HCl, HNO3 and H2SO4 are implicated in atmospheric processes in areas such as polar stratospheric clouds in the stratosphere. Ternary complexes of HCl, HNO3 and H2SO4 were investigated by ab initio calculations at B3LYP level of theory with aug-cc-pVTZ and aug-cc-pVQZ basis sets, taking into account basis set superposition error (BSSE). The results were assessed in terms of structures (five hexagonal cyclic structures and two quasi-pentagonal cyclic structures), inter-monomeric parameters (all ternary complexes built three hydrogen bonds), energetics (seven minima obtained), infrared harmonic vibrational frequencies (red shifting of complexes from monomers), and relative stability of complexes, which were favorable when the temperature decreases under stratospheric conditions, from 298K to 188K, and in concrete, at 210K, 195K and 188K.

On the gas-phase OsOn+ (n = 0–3) catalyzed reduction of N2O by H2: A density functional study

The mechanisms of the reactions between N2O and H2 catalyzed by OsOn+ (n=0–3) on quartet and sextet electronic state have been investigated using B3LYP levels of theory. Geometries and energies of all the stationary points involved in the catalytic reaction are located. All the transition states were verified by the vibrational analysis and the intrinsic reaction coordinate calculations. From the values of O-atom affinities, we obtained that the OsOn+ (n=0–3) have good O-transfer function from N2O to H2. Our calculated results indicate that the reaction pathways are all very similar on two potential energy surfaces, and the mechanism corresponding to the O-atom transfer reaction. These results are in good agreement with experimental observations.

Bismuth(III) halides as halide source for preparation of dihaloplatinum(IV) complexes

The complexes [PtMe2(tBu2bpy)], 1a, tBu2bpy=4,4′-di-tert butyl-2,2′-bipyridine, and [PtMe(ppy)PPh3], 1b, ppy=deprotonated 2-phenylpyridine, react very easily with BiX3 (X=Cl, Br, or I) to give [PtMe2(X)2(tBu2bpy)] (2a, X=Cl; 3a, X=Br; 4a, X=I) and [PtMe(X)2(ppy)PPh3] (2b, X=Cl; 3b, X=Br; 4b, X=I), respectively. In these oxidative addition reactions, BiX3 reagent can be used as halide source instead of hazardous reagents X2. The dihaloplatinum(IV) complexes are characterized using NMR spectroscopy and the structures of complexes 4a and 3b are further identified by X-ray crystallography. Structures of Pt(IV) complexes are investigated using DFT calculations at B3LYP level of theory.

Thermodynamic study of 2-aminothiazole and 2-aminobenzothiazole: Experimental and computational approaches

This work reports an experimental and computational thermochemical study of two aminothiazole derivatives, namely 2-aminothiazole and 2-aminobenzothiazole.The standard (p°=0.1MPa) molar energies of combustion of these compounds were measured by rotating bomb combustion calorimetry. The standard molar enthalpies of sublimation, at T=298.15K, were derived from the temperature dependence of the vapor pressures of these compounds, measured by the Knudsen-effusion technique and from high temperature Calvet microcalorimetry. The conjugation of these experimental results enabled the calculation of the standard molar enthalpies of formation in the gaseous state, at T=298.15K, for the compounds studied. The corresponding standard Gibbs free energies of formation in crystalline and gaseous phases were also derived, allowing the analysis of their stability, in these phases.We have also estimated the gas-phase enthalpies of formation from high-level molecular orbital calculations at the G3(MP2)//B3LYP level of theory, the estimates revealing very good agreement with the experimental ones.The importance of some stabilizing electronic interactions occurring in the title molecules has been studied and quantitatively evaluated through Natural Bonding Orbital (NBO) of the corresponding wavefunctions and their Nucleus Independent Chemical Shifts (NICS) parameters have been calculated in order to rationalize the effect of electronic delocalization upon stability.

Theoretical investigation for the cycle reaction of methane oxidation catalyzed by FeO<sup>+</sup> in the gas phase

The mechanism of the spin-forbidden reaction of CH4 with O2 catalyzed by FeO+ (6Σ+, 4Π+) on both quartet and sextet potential energy surfaces has been investigated at the B3LYP level of theory. Six competitive reaction pathways for the catalytic reaction and Path 6 are likely in competition with other pathways from energetic viewpoint. There are 6 crossing points in Path 6 and the crossing points 1 and 3 are very important. The minimum energy crossing points (MECP) of corresponding crossing points are optimized. The potential energy surfaces and the possible spin inversion processes are discussed by means of spin-orbit coupling (SOC) and probability of intersystem crossing (ISC) calculations. The SOC of MECP1 is 947.58 cm-1, and MECP3 is 1372.51 cm-1. The probability of ISC are 0.535 and 0.590 respectively. In order to understand the competitive reaction mechanism involving H atom transfer, the activation strain model was adopted for a simple analysis of the competitive reaction. The energetic span ( δE ) model coined by Kozuch is applied in this cycle. X TOF (degree of TOF control) of all of transition state and intermediate are calculated, and the turnover frequency (TOF)-determining transition state (TDTS) and TOF-determining intermediate (TDI) are confirmed. In this catalytic reaction, the TOF is 5.6716×10-42 s-1.

Time-Resolved IR Spectroscopy of 1,3-Dicyanophenylcyclopentane-1,3-diyl Diradicals: CN Stretching Wavenumber as a Vibrational Signature of Radical Character

CN stretch bands of singlet and triplet cyclopentane-1,3-diyl diradicals (1,3-di(4-cyanophenyl)-2,2-dimethoxyoctahydropentalene-1,3-diyl and 1,3-di(4-cyanophenyl)-2,2-dimethyloctahydropentalene-1,3-diyl) were observed by time-resolved IR spectroscopy. CN stretching wavenumbers of the singlet and triplet diradicals were downshifted by 10 and 19 cm(-1) from those of their corresponding ring-closed compounds, which are in closed-shell electronic states, respectively. The observed downshifts are attributed to the bond-order decrease in the CN bonds due to the contribution from a resonance structure that has cumulative double bonds (C ═ C ═ N(•)) at the para-positions of the radical carbons. This resonance structure is only possible when the molecules have unpaired electrons; thus, the wavenumber downshift can be regarded as an experimental manifestation of the radical character of the diradicals. The observed CN stretching wavenumbers indicate that the radical character of the singlet diradical is less significant than that of the triplet. The smaller radical character is ascribed to the contribution from the zwitterionic and π-single bonding resonance structures in the singlet diradical. Unrestricted DFT calculations at the B3LYP level of theory with the 6-31G(d) basis set reproduced the small/large relationship between the wavenumber downshifts of the singlet and triplet diradicals; however, the shift of the singlet diradical was overestimated.

Quantum mechanical and spectroscopic (FT-IR, 13C, 1H NMR and UV) investigations of 2-(5-(4-Chlorophenyl)-3-(pyridin-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole by DFT method

The electronic, NMR, vibrational, structural properties of a new pyrazoline derivative: 2-(5-(4-Chlorophenyl)-3-(pyridine-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole has been studied using Gaussian 09 software package. Using VEDA 4 program we have reported the PED potential energy distribution of normal mode of vibrations of the title compound. We have also reported the 1H and 13C NMR chemical shifts of the title compound using B3LYP level of theory with 6-311++G(2d,2p) basis set. Using time dependent (TD-DFT) approach electronic properties such as HOMO and LUMO energies, electronic spectrum of the title compound has been studied and reported. NBO analysis and MEP surface mapping has also been calculated and reported using ab initio methods.

DFT study on the isomerization in vitamin B6

Isomerization and tautomerism reactions of the active form of vitamin B6, pyridoxal phosphate, are studied at B3LYP level of theory using 6-311++G(2df,p) basis set in gas and aqueous phases. Twenty-three transition state (TS) structures for vitamin B6 isomerization are optimized, including 13 TS structures for O–H and C–C rotations, 8 TS structures for imine–enamine tautomerism, and 2 TS structures for keto–enol tautomerism. Activation energy (E a), imaginary frequency (υ), and Gibbs free energy of activation (ΔG #) for the isomerization reactions are calculated. The activation energies of the imine–enamine tautomerism are in the range of 190–280 kJ/mol and of O–H and C–C rotations are mainly less than 60 kJ/mol. Also, our calculation shows that the imine forms of B6 are mainly more stable than the enamine forms. Effect of microhydration on the TS structures and activation energies is also investigated. It is found that the presence of water molecules catalyzes only the imine–enamine tautomerism.

PREDICTION OF REACTION RATE CONSTANTS OF HYDROXYL RADICAL WITH ORGANIC COMPOUNDS

In this work we have performed a QSAR study of atmospheric reactions with hydroxyl radical, at the B3LYP level of theory with 6-31G(d) basis set. Molecular descriptors selected by applying multiple linear stepwise regression (MLR) analysis were used to predict the reaction rate constants (-logkOH) of OH radicals with organic compounds in the atmosphere, including 98 alkenes and 80 aromatic compounds. For setting our reactions, we have calculated 98 alkenes and 80 aromatic compounds. A four-descriptor MLR model (rms = 0.102 and R2= 0.938) for 98 alkenes was developed based on the number of R=CHX functional group counts, EHOMO parameter, and Fukui indices of the double-bonded C atoms. We found vinyl chemicals with conjugated double bonds and electron-donor substituents are the most reactive systems; while alkenes with multiple halogen substitutions are the least reactive molecules. Additionally, a three-descriptor MLR model (rms = 0.282 and R2= 0.910) was built to predict OH radical rate constants for 80 aromatic compounds, which was dominated by the EHOMO parameter, a topological descriptor for steric hindrance, and the most positive net atomic charge on hydrogen atoms. Aromatics with electron-donor and electron-acceptor groups, respectively, possess high and low degradation rates. The halogen aromatics are less reactive, especially for aromatics with multiple halogen substitutions. In comparison to existing models, the two models obtained in this paper show better statistical quality.

Molecular Dynamics of Methanol Monocation (CH3OH+) in Strong Laser Fields

Experimental studies by Yamanouchi and co-workers indicate that an intense 40 fs 800 nm laser pulse can cause CH3OH(+) to isomerizes during the pulse. The potential energy surfaces of methanol neutral, monocation, and singlet and triplet dication were explored using the CBS-APNO, CBS-QB3, CAM-B3LYP, and B3LYP levels of theory. Ab initio classical trajectories were calculated in the presence of a 2.9 × 10(14) W/cm(2) 800 nm laser field for methanol monocation on the ground state potential energy surface using the CAM-B3LYP/6-31G(d,p) level of theory. With only zero point energy, CH3OH(+) gained less than 15 kcal/mol from the 40 fs laser pulse, which was not enough to overcome any of the barriers for isomerization or fragmentation. To simulate extra energy deposited during the ionization process, 75, 100, and 125 kcal/mol of vibrational energy was added to the initial structures. After 400 fs, the distribution of product was CH2OH(+) + H (79-81%), HCOH(+) + H2 (9-13%), CH2OH2(+) (1-3%), CH3(+) + OH (1-3%), and CH2(+) + H2O (<0.5%). The estimated kinetic energy releases are in accord with experimental findings. Experimental results using a probe pulse to ionize CH3OH(+) to the dication showed substantial fraction C-O dissociation in both CH3OH(+) and CH2OH2(+) after the pulse. Because very few CH2OH2(+) → CH2(+) + H2O trajectories were seen in the simulation, the calculations suggest that some of the processes observed experimentally must occur on excited state surfaces or may be due to coupled nuclear-electron dynamics during the pump pulse.

High level ab initio, DFT, and RRKM calculations for the unimolecular decomposition reaction of ethylamine

Mechanisms for the decomposition reaction of ethylamine, CH3CH2NH2, were investigated using ab initio, DFT, and RRKM calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at HF, MP2, and B3LYP levels of theory using the 6-31G(d) and 6-31+G(d) basis sets. Single point energies were also determined at G3MP2B3 and G3B3 levels of theory. Thermodynamic properties, activation energies, enthalpies and Gibbs energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. The conformational change and planarity of the ethylamine moiety along with the twist angle of the amino group about the CN axis are examined. Four pathways for the decomposition reaction of ethylamine were studied. All pathways involve a 1,2-elimination reaction and 1,3-proton shift to produce ethene, ethanimine, ethenamine, and methanimine. All pathways are single-step mechanisms. Elimination of the NH3 dominates the decomposition behavior up to 1200K whereas after this temperature, secession of the C–N gradually holds more importance. While pathways signifying departures of NH3 and NH2 exhibit pressure-dependent behavior, branching ratios for these two channels are generally not influenced by variation in pressure higher than the atmospheric pressure.

A study of the conformational profile and the vibrational spectra of the plant hormone indole-3-acetic acid

The structural stability of indole-3-acetic acid was investigated by DFT-B3LYP calculations with the 6-311G** basis set. From the calculations the gauche–gauche (gg) structure was predicted to be the second lowest energy minimum for the acid. It is energetically only 0.57 kcal/mol above the lowest conformer which is the trans–cis (tc) structure. A further stable conformer, however, highest in energy, is the trans–trans (tt) one, which is by 2.68 kcal/mol higher in energy than tc. The tc conformer upon full optimization turned a little bit away from real tc to a near tc (ntc) structure (defining torsional angles only changed by a few decigrades). However, the X-ray data indicate a structure in the solid, which is most similar to gg, stabilized by intermolecular eight ring hydrogen bonds. In the present DFT calculations such stabilizations cannot be accounted for, because the calculations treat only isolated molecules. To take such interactions into account at least dimers would have to be optimized. Therefore the vibrational frequencies of the gg conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis, normal mode calculations and experimental infrared and Raman data. However, some of the observed lines are obviously due to a small amount of the tc conformer present.

Computational study of structural properties of lithium cation complexes with carbamate-modified disiloxanes

Lithium cation solvation structures [Li(S)(n=1-4)](+) with ligands of cyclic or noncyclic carbamate-modified disiloxanes are optimized at B3LYP level of theory and compared to their corresponding simplified carbamates and to the organic carbonates ethylene carbonate (EC) and dimethyl carbonate (DMC). The electrostatic potentials (ESP) of these investigated carbonyl-containing solvents are mapped on the electron density surface. The maximum ESP is located at the C=O-oxygen, whereas the disiloxane functionality represents an unpolar residue. Natural Bond Orbitals (NBO) analysis reveals strong n(N) →π(C[double bond, length as m-dash]O) donor-acceptor interactions in carbamates which outrun dipolar properties. As a result, higher total binding energies (ΔE(B)) for solvation of Li(+) in carbamates (-148 kcal mol(-1)) are found than for carbonates (-137 kcal mol(-1)). Furthermore, the disiloxane moiety with its Si-O bond is stabilized by n(O) →σ*(Si-C) hyperconjugation that provides additional electron density to a nearby SiCH3 methyl group thus supporting an additional SiCH2-H...Li(+) coordination. The formation of all investigated solvation structures is exothermic. Owing to steric hindrance of noncyclic carbonyl-containing ligands and the bulky disiloxane functionality, the solvation structure [Li(S)3](+) is the preferred structure according to Gibbs free energy ΔG(B) results.

Ab initio studies on the proton dissociation and infrared spectra of sulfonated poly(ether ether ketone) (SPEEK) membranes

SPEEK is known to possess high proton conductivity at high water content, being comparable with other popular membranes used in fuel cells, such as Nafion and sulfonated polyethersulfone (SPES). However, much less is known about its fundamental properties, including the status of proton dissociation and spectral features. In this work, the properties of two model molecules of SPEEK, M1 (20 atoms), M2 (50 atoms) and their hydrated systems, M1 + nH2O and M2 + nH2O (n = 1-9), have been investigated using static electronic structure calculations and the ab initio molecular dynamics (MD) method. Optimized structures for all of the systems and the trajectories of M1 + nH2O (n = 3-6) at finite temperatures have been computed using density functional theory at the B3LYP level of theory. Proton dissociation has been discussed in detail, especially for n = 3 and n = 4. In addition, the infrared spectra of SPEEK and its hydrated systems have been studied using a combination of theory and experiment. The characteristic bands of SPEEK and the surrounding water clusters have been assigned with emphasis on their relationship with the degree of proton dissociation. We have found that the hydronium ion stretching modes, which appear in the 2000-3000 cm(-1) region in static electronic structure calculations, are not observed experimentally. This discrepancy is explained by the stationary structure and the temperature effect.