Density Functional B3LYP Method Research Articles

π-Hydrogen Bonding Probes the Reactivity of Aromatic Compounds: Nitration of Substituted Benzenes.

The shifts of phenol O-H stretching vibration frequencies [Δν(OH)exp] upon π-hydrogen bonding with aromatic compounds is proposed as a spectroscopic probe of the reactivity of aromatic substrates toward electrophiles. A single infrared spectrum reflecting the Δν(OH)exp shift for an aromatic species in a reference solvent (CCl4 in this study) provides a good estimate of reactivity. The methodology is applied in rationalizing reactivity trends for the BF3 catalyzed nitration by methylnitrate in nitromethane of 20 aromatic reactants, including benzene, 11 methylbenzenes, several monoalkyl benzenes, the four halobenzenes, and anisole. Literature kinetic data are employed in the analysis. Very good correlations between relative rates of nitration and Δν(OH)exp are obtained. The approach is best applied to reactions, where the initial interactions between the reactants controls the rates. A new theoretical quantity, the shifts (with respect to benzene) of the molecular electrostatic potential at 1.5 Å over the centroid of the aromatic ring [Δ V(1.5)] is defined and shown to provide a good description of substituent effects on properties of the aromatic species. B3LYP density functional and MP2 ab initio methods combined with the 6-311++G(3df,2pd) basis set are employed in evaluating the Δ V(1.5) values.

Structure, Reactivity, Nonlinear Optical Properties and Vibrational Study of 5-Thioxo-1,4-thiazaolidin-3-one and 5-thioxo-1,4,2-thiazasilolidin-3-one (Silicon vs. Carbon). A DFT Study

The structures and nonlinear optical properties (NLO) of 5-thioxo-1,4-thiazaolidin-3-one(Rhodanine) and 5-thioxo-1,4,2-thiazasilolidin-3-one (silarhodanine) tautomers were studied in gas phase and in solutions using the B3LYP density functional theory and composite CBS-QB3 method. The global minimum at the B3LYP/6-31++G(d,p) and CBS-QB3 levels of theory is tautomer 5 in the gas phase and in solvents for rhodanine, and simiarly, tautomer 13 is the global minimum for silarhodanine. The interconversion among the tautomers is proceeded by an intramolecular proton transfer reaction. An identical solvent effects can be noted for rhodanine and silarhodanine tautomers. The activation barrier towards ring-opening processes (1→2, 9→10) decreases with the increasing dielectric constant of the solvent; on the other hand, the barrier of the ring-closure processes (2→3, 10→11) increases with the increasing dielectric constant. The tautomers are predicted to show significant NLO properties. Also, a number of correlations between the dipole moment and electron densities in bond critical points of the S3-C4 bond and interaction energy as well as vibrational frequencies at the transition states (TS2–3,TS10–11) were examined under different solvents. Finally, the investigation of the heavy atom substitution effects on the properties of silarhodanine is proven to be very weak under these conditions.

Оптимальность и точность компьютерных вычислений свободной энергии Гиббса гидратации молекул в континуальных моделях сольватации

  In this paper, computer simulations of dissolving some small organic molecules: methanol (CH3OH), ethanol (CH5OH), acetamide (H3CC(O)NH2), methanethiol (CH3SH), methylamine (CH3NH2), chloromethane (CH3Cl) in water and calculations of the Gibbs free energy of hydration are performed. Calculations of the free energy of hydration are carried out within the framework of two well-known continuum solvation models: Solvation Model of Density (SMD) and Conductor-like Polarizable Continuum Model (CPCM). The quantum-mechanical part of the calculations is performed by the method of the hybrid density functional b3lyp and the restricted Hartree-Fock method. A comparative assessment of the accuracy and timing of calculations using different methods has been carried out. The versatility, high accuracy, and low consumption of calculation time using the SMD in a frame of the density functional method b3lyp are shown. In comparison with experimental data, errors of the values of the free Gibbs energy of dissolution of molecules in water are not exceeded 20 percent. The two modified CPCM models demonstrate worse results regarding accuracy and time consumption than the SMD approach. In this case, the restricted Hartree-Fock method turns out to be preferable compared to the density functional method b3lyp.

The symmetry breaking phenomenon in heteronine analogues due to the pseudo Jahn-Teller effect.

The pseudo Jahn-Teller effect (PJTE) is employed in C8AH8 (A = O, S, Se, Te), and C8EH8 + 1 (E = N, P, As, Sb) with planar configurations to show symmetry breaking phenomena (SBP) in heteronine analogues, and to explain why molecules with (C2v) high-symmetry configurations cannot maintain planarity and pucker to their (C2) and (Cs) lower-symmetry structures, respectively. To investigate this phenomenon, geometry optimization and frequency calculations through the density functional B3LYP method using the cc-pVTZ basis set (for Te, and Sb cc-pVTZ-PP) were carried out for all compounds in the series. The state average-complete active space self-consistent field wave-function method was employed to calculate the electronic ground and several low-lying excited states to specify the adiabatic potential energy surface along the a2 and b1 puckering nuclear displacements. The PJTE (A1 + A2 + A1') a2 and (A1 + B1 + A1') b1 problems were formulated as the effects originating via the PJTE theorem. Moreover, replacing hydrogen atoms in C8NH9, a stable planar structure, with fluorine ligands demonstrated that SBP occur from C2v to C2 symmetry. Furthermore, thermochemical calculations via B3LY/cc-pVTZ illustrated that the planarity of the C8E ring is restored in C8EH8- (E = P, As, Sb) anions ,with the change in free energy corresponding to spontaneous deprotonation reactions as 23.67kJmol-1, 21.88kJmol-1, and 16.57kJmol-1, respectively. In fact, despite C8EH8 + 1 having a donor electron-pair and potentially being Lewis base compounds, it acts as a Bronsted-Lowry acid releasing a H+ proton instead in this case.

Novel Triazole Thiole ligand and some of its metal chelates: Synthesis, structure charactertization, thermal behavior in comparison withcomputational caculations andbiological activities

Structural and molecular properties of HL, 4-amino-5-(2,2-dichloro-1-methylcyclopropyl)-4H-1,2,4-triazole-3-thiol toward the transition metal ions namely Fe(III), Co(II) and Ni(II) had been studied using elemental analyses, magnetic, electronic, FT- IR, 1H-NMR and Thermal analyses (TGA and DTA). The interpretation of thermal decomposition stages had been evaluated. The computations had been done by software of Gaussian 09W package. The geometries of triazole-thiole ligand and its metal chelates were fully optimized using density functional theory B3LYP method. (DFT)/GENECP level by implementing Def2TZVP basis set was used for Fe, Co and Ni-atoms; and basis set 6-311++G (d, p) was used for remainder atoms. There are no symmetry constrains had been applied during geometry optimization. The mixed basis set was selected due to its flexibility. HOMO and LUMO energy values for chelates, chemical hardness and electronegativity had been calculated. NBO calculations had been done at the same level using (NBO 3.1) program involved in the software of Gaussian 09W for measurement qualitatively the intra-molecular delocalization in systems under investigation. The first 15, 85, 65 and 65 low-lying excited states for ligand and Fe, Co and Ni chelates respectively had been calculated within the vertical linear-response. TD-DFT approximation at the same level of theory was used to calculate the electronic absorption spectra of the studied compounds. Their structures are confirmed by successful correlation between experimental and theoretical calculations. The ligand and its metal chelates had been examined against two bacteria such as Gram-positive (Staphylococcus aureus ATTC 12600), GraM–Negative (Escherichia coli ATTC 11775) and two fungus (Aspergillus flavus and Candida albicans) and molecular docking using Auto Dock tools were utilized.

Molecular modelling and vibrational investigations of ammonium-based ionic liquid (CLTOAB)

CLTOAB is an ammonium-based ionic liquid composed of ε-Caprolactam (CL) C6H11NO and tetraoctylammonium bromide (TOAB) (C32H68BrN). In this study, experimental IR and Raman spectra of CLTOAB ionic liquid together with the computational results of the compound have been reported. The optimized geometry, vibrational frequencies, IR intensities and Raman activities of the CLTOAB were calculated using the wb97xd and B3LYP density functional methods combined with the 6-31G(d,p) basis set using Gaussian 03 program. The complete assignment of the bands was performed based on the potential energy distributions (PED%). The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The Gauge-including atomic orbital 1H-NMR and 13C-NMR chemical shifts calculations were carried out and compared with the experimental data. Furthermore to evaluate interaction between CLTOAB and DNA, molecular docking study was carried out.Communicated by Ramaswamy H. Sarma

Synthesis, crystal structure and NLO study of two new versatile Ca (II) complexes

Two new versatile supramolecular calcium complexes [Ca2(NPG)4(1,10 phen)2] (1) and [Ca2(NPß‐ala)4(1,10 phen)2] (2) have been synthesized by the addition of 1,10‐phenanthroline to the solution of already prepared corresponding calcium N‐phthaloylglycinate and calcium N‐phthaloyl‐β‐alaninate complexes, which were prepared from the reaction of calcium oxide with N‐phthaloylglycine (NPG) and N‐phthaloyl‐β‐alanine (NPß‐ala), respectively. The complexes were characterized by single X‐ray diffraction method. The spectroscopic and electronic properties were investigated by utilizing Fourier transform‐infrared and UV–Vis spectroscopic techniques. The theoretical calculations were performed by using B3LYP‐D3 method (standard hybrid density functional B3LYP method with dispersion correction D3) to find the coherent relationship between experimental and theoretical findings for structural, spectroscopic and electronic properties. The natural bond orbital analysis was performed for both complexes to study charge transfer. The solid state photoluminescence for both Ca complexes was observed experimentally. The nonlinear optical (NLO) properties of both complexes have been analyzed theoretically, and it was found that both Ca complexes showed excellent NLO prospective potential as compared with the commercial NLO active materials like para‐nitrotoluene (PNA) and urea. Further, it was concluded that 2 showed much more increase in first static hyperpolarizabilty as compared with 1.

Theoretical Study of the Formation Methane in the Reaction of Methyl Radical with Propanol-2

Theoretical Study of the Formation Methane in the Reaction of Methyl Radical with Propanol-2

Theoretical Study on Reaction Pathways of Methyl Radical with Ethylamine

Theoretical Study on Reaction Pathways of Methyl Radical with Ethylamine

Phosphate-Catalyzed Succinimide Formation from an NGR-Containing Cyclic Peptide: A Novel Mechanism for Deammoniation of the Tetrahedral Intermediate.

Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an isoAsp-Gly-Arg (isoDGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur via the five-membered ring succinimide intermediate. Recently, we computationally showed by the B3LYP density functional theory method, that inorganic phosphate and the Arg side chain can catalyze the NGR deamidation using a cyclic peptide, c[CH2CO–NGRC]–NH2. In this previous study, the tetrahedral intermediate of the succinimide formation was assumed to be readily protonated at the nitrogen originating from the Asn side chain by the solvent water before the release of an NH3 molecule. In the present study, we found a new mechanism for the decomposition of the tetrahedral intermediate that does not require the protonation by an external proton source. The computational method is the same as in the previous study. In the new mechanism, the release of an NH3 molecule occurs after a proton exchange between the peptide and the phosphate and conformational changes. The rate-determining step of the overall reaction course is the previously reported first step, i.e., the cyclization to form the tetrahedral intermediate.

Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP

The calcium-dependent β-propeller proteins mammalian serum paraoxonase 1 (PON1) and phosphotriesterase diisopropyl fluorophosphatase (DFPase) catalyze the hydrolysis of organophosphorus compounds and enhance hydrolysis of various nerve agents. In the present work, the phosphotriesterase activity development between PON1 and DFPase was investigated by using the hybrid density functional theory method B3LYP. Based on the active-site difference between PON1 and DFPase, both the wild type and the mutant (a water molecule replacing Asn270 in PON1) models were designed. The results indicated that the substitution of a water molecule for Asn270 in PON1 had little effect on the enzyme activity in kinetics, while being more efficient in thermodynamics, which is essential for DFP hydrolysis. Structure comparisons of evolutionarily related enzymes show that the mutation of Asn270 leads to the catalytic Ca2+ ion indirectly connecting the buried structural Ca2+ ion via hydrogen bonds in DFPase. It can reduce the plasticity of enzymatic structure, and possibly change the substrate preference from paraoxon to DFP, which implies an evolutionary transition from mono- to dinuclear catalytic centers. Our studies shed light on the investigation of enzyme catalysis mechanism from an evolutionary perspective.

Synthesis, spectroscopic characterization, anti-urease activities of a novel bisphosphoramidate, a combined experimental and computational study

Methylenebis(N,N′-dibenzylphosphoramidate) (MBDPA) is synthesized by 1:8 mol ratio reaction of Methylenebis(phosphonic dichloride) and benzylamine. MBDPA characterized by FT-IR, 1H NMR, 13C NMR, 31PNMR spectroscopy. Also, The IC50 value for MBDPA is 5.23 nM that show very strong urease inhibitory activity. The geometry optimization is performed using the B3LYP and PBE1PBE density functional methods with two basis sets; 6–311 G (d, p) and 6-311 + G(d,p). 1H, 13C and 31PNMR chemical shifts have been calculated by using the gauge independent atomic orbital (GIAO) method. The infrared spectra of MBDPA are calculated and compared with the experimentally observed ones. The assignments are determined on the basis of the potential energy distribution of the all vibrational modes. Results of this study showed that there is a good correlation between the experimental data and computational results. The electronic structure is studied by analyzing the frontier molecular orbitals and molecular electrostatic potential for the prediction of stability and activity of the MBDPA.

Analysis on molecular, spectroscopic and electronic behavior of 4,4'-(butane-1,4-diyl)bis(1-((1-(4-chlorobenzyl)-1H-1,2,3-triazol-5-yl)methyl)-3-methyl-1H-1,2,4-triazol-5(4H)-one): A theoretical approach

In this study, 4,4'-(butane-1,4-diyl)bis(1-((1-(4-chlorobenzyl)-1H-1,2,3-triazol-5-yl)methyl)-3-methyl-1H-1,2,4-triazol-5(4H)-one) was synthesized and characterized by FT-IR, 1H NMR and 13C NMR. In addition, quantum chemical calculations of the structure, vibrational frequencies, gauge including atomic orbital 1H and 13C chemical shift values were carried out using the density functional B3LYP method with the 6-311++G(d,p) basis set. To investigate nonlinear optical properties of the compound, the dipole moment, the polarizability and the first hyperpolarizability were computed using the density functional B3LYP and Hartree-Fock methods with the 6-311++G(d,p) basis set. Besides, density functional theory calculations of the molecular electrostatic potential, frontier orbitals and atomic charges of the compound were carried out at the B3LYP/6-311++G(d,p) level of theory.

Energy transfer or electron transfer?—DFT study on the mechanism of [2+2] cycloadditions induced by visible light photocatalysts

The intramolecular [2+2] cycloaddition of 1,3-dienes under visible light irradiation investigated by Yoon and his co-workers shows remarkably high yield and stereoselective differences under different photocatalysts. The reaction was speculated to be induced by energy transfer. However, the origin for these phenomena is still unclear. In this scene, the detailed mechanism for the [2+2] cycloaddition of 1,3-dienes under visible light has been investigated using density functional theory B3LYP and TPSSTPSS methods. The result shows that the reaction not only can be induced by energy transfer between photocatalysts and reactants, but also can be induced by electron transfer between them. The [2+2] cycloaddition induced by energy transfer is carried out along the potential energy surface (PES) of triplet excited states (T1) firstly, and then goes back to the singlet ground state (S0) via MECPs (minimum energy crossing points) between the PESs of the S0 and T1 states, forming the product in the S0 state. The [2+2] reaction induced by electron transfer proceeds along the doublet state PES of the cation radical reactant and the neutral four-membered ring product could be obtained by electron transfer from the corresponding reactant or reduced photocatalyst. The origin of stereoselectivity of the [2+2] reaction is attributed to the reaction mechanism difference under different photocatalysts.

Molecular simulation and experimental study on thermal decomposition of N,N′-dinitrosopentamethylenetetramine

N,N′-dinitrosopentamethylenetetramine (DNPT), which is a widely used as blowing agent in the rubber industry, tends to be unstable when affected by high temperature and specific impurities. The runaway of DNPT has caused several accidents and led to enormous economic losses in the world. We determined its thermal hazard properties and decomposition paths for process safety. Characteristic parameters of pure and impure (added with water and nitric acid) DNPT were obtained under different heating rates by differential scanning calorimetry experiments. Those parameters were used to calculate the apparent activation energy with the Kissinger method. Thermogravimetry was used to obtain exothermic onset temperature and peak temperature under different heating rates. The apparent activation energy of DNPT decomposition reaction was achieved by model-free kinetics approach. Quantum mechanics model was used to explore the thermal decomposition reaction pathways of DNPT. DFT B3LYP density functional method, and the 6-311++G (D) basis set was selected for molecular simulation by Gaussian 09 software. The single point energy, zero-point energy, thermal energy, thermal enthalpy, and thermal free energy were acquired. The bond dissociation energy (BDE) at different excited states was calculated. By comparing BDE of different excited states, the thermal decomposition reaction pathways can be predicted. The results of experiments and simulations can be applied as safety guidance to deal with DNPT’s loss prevention during transportation, handling, and storage, even emergency response.

Prediction of the electron redundant SinNn fullerenes

The stabilities and electronic structures of SimAln-mNn and SinNn (n = 16, 20, m = 12 and n = 24, m = 16) fullerene-like cages have been investigated using density functional method B3LYP and the second-order perturbation theory MP2. The results show that the SimAln-mNn and SinNn fullerenes are more stable than the AlN counterparts. Comparing with the corresponding AlnNn cages, one silicon atom in each Si2N2 square protrudes and the excess electrons reside as lone pair electrons at the outside of the protrudent Si atoms. Analyses on the electronic structures suggest that the SiN bonds are covalent bonding with strong polarity. The ELF (electron localization function) shows large electron pair probability between Si and N atoms. The orbital interactions between Si and N are stronger than that between Al and N atoms; the overlap integral is 0.40 per SiN bond in SinNn and 0.34 per AlN bond in AlnNn. The AIM (atoms in molecule) charges on the Al atoms in AlnNn and SimAln-mNn are 2.37 and 2.40. The charges on the in-plane and protrudent Si atoms are about 2.88 and 1.50 respectively. Considering the large local dipole moments around the protrudent Si atoms, the electrostatic interactions are also favorable to the SiN cages.

Vibrational spectroscopic (FT-IR, FT-Raman) and quantum mechanical study of 4-(2-chlorophenyl)-2-ethyl-9-methyl-6H-thieno[3,2-f] [1,2,4]triazolo[4,3-a][1,4] diazepine

The spectroscopic properties of 4-(2-chlorophenyl)-2-ethyl-9-methyl-6H-thieno [3,2-f] [1,2,4] triazolo [4,3-a] [1,4] diazepine were investigated in the present study using FT-IR and FT-Raman techniques. The results obtained were compared with quantum mechanical methods, as it serves as an important tool in interpreting and predicting vibrational spectra. The optimized molecular geometry, the vibrational wavenumbers, the infrared intensities and Raman scattering were calculated using density functional theory B3LYP method with 6–311++g (d,p) basis set. All the experimental results were in line with the theoretical data. The molecular electrostatic potential (MEP) and HOMO LUMO energies of the title compound were accounted. The results indicated that the title compound has a lower softness value (0.27) and high electrophilicity index (4.98) hence describing its biological activity. Further, natural bond orbital was also analyzed as part of the work. Fukui functions were calculated in order to explain the chemical selectivity or the reactivity site in 4-(2-chlorophenyl)-2-ethyl-9-methyl-6H-thieno [3,2-f] [1,2,4] triazolo [4,3-a] [1,4] diazepine. The thermodynamic properties of the title compound were closely examined at different temperatures. It revealed the correlations between heat capacity (C), entropy (S) and enthalpy changes (H) with temperatures. The paper further explains that the title compound can act as good antidepressant through molecular docking studies.

Probing structure, thermochemistry, electron affinity, and magnetic moment of thulium-doped silicon clusters TmSi n (n = 3-10) and their anions with density functional theory.

The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi n (n = 3-10) and their anions do not participate in bonding. The total magnetic moments of TmSi n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi n and their anions has been calculated to examine relative stability.

Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study

Spontaneous, nonenzymatic reactions in proteins are known to have relevance to aging and age-related diseases, such as cataract and Alzheimer’s disease. Among such reactions is the racemization of Ser residues, but its mechanism in vivo remains to be clarified. The most likely intermediate is an enol. Although being nonenzymatic, the enolization would need to be catalyzed to occur at a biologically relevant rate. In the present study, we computationally found plausible reaction pathways for the enolization of a Ser residue where a dihydrogen phosphate ion, H2PO4−, acts as a catalyst. The H2PO4− ion mediates the proton transfer required for the enolization by acting simultaneously as both a general base and a general acid. Using the B3LYP density functional theory method, reaction pathways were located in the gas phase and hydration effects were evaluated by single-point calculations using the SM8 continuum model. The activation barriers calculated for the reaction pathways found were around 100 kJ mol−1, which is consistent with spontaneous reactions occurring at physiological temperature. Our results are also consistent with experimental observations that Ser residue racemization occurs more readily in flexible regions in proteins.

Molecular structure, X-ray crystallography, spectroscopic characterization, solvent effect, NLO, NBO, FMO analysis of [Cu(bpabza)] complexe

In this work, first, the new asymmetric carboxamide ligand of (H2bpabza) was synthesized in the laboratory and it was used to make [Cu(bpabza)] complex. Then, FT IR and NMR spectra and X-ray crystallography were used to examine the structure of tetradentate ligand N,N′-bis (2-pyridinecarboxamide)-2-aminobenzylamine (H2bpabza) and Cu(II) complex. Next, the structure of ligand and the resulting complex were drawn using Chembio Draw Ultra software and powerful Gaussian 09 software, computational methods of Density Functional Theory (DFT), B3LYP and MPW1PW91 methods with LanL2DZ basis set were used to study the structure of ligand and Cu(II) complex, to optimize them and to examine the bond length and the bond angle and these values were compared with experimental values.Then, polarizability of its atoms was calculated using Mulliken charge and natural atomic charges. Stretching and bending vibrations were calculated by FT IR and were compared with experimental values. Also, the chemical shift of carbons and hydrogens were calculated using Nuclear Magnetic Resonance (NMR). Donor-acceptor interactions and Hyperpolarizability calculations were used to determine the type of electron transfers and the amount of global hardness (η) and global softness (S) of molecule were calculated using the energy difference between the highest occupied molecular orbital (HOMO) to the Lowest unoccupied molecular orbital (LUMO) in the presence of solvents CH3OH, DMSO, C6H6 and CHCl3. Also UV–Vis spectra were calculated in the presence of solvents CH3OH, DMSO, C6H6 and CHCl3. DFT/B3LYP and MPW1PW91 methods with LanL2DZ basis set were used in all computational methods.