B3LYP Calculations Research Articles

Quantum-Chemical Study of Stressed Polyethylene and Butadiene Rubber Chain Scission

The thermal decomposition of polyethylene and butadiene rubber chains in the presence of a tensile force acting along the axis of the molecule was simulated. The reaction of an isolated chain was considered. The chain models were the octane and 2,6-octadiene molecules. A deformation was introduced in the problem by fixing nonequilibrium distances between the terminal carbon atoms. The reaction coordinate (the middle C–C bond length R) was scanned at a fixed length of the molecule (L). That is, the potential energy surface section of the reaction was constructed at L = const. The reaction sensitivity to deformation was evaluated by B3LYP, LC-ωPBE, CCSD(T), CASSCF, and MP2 quantum-chemical calculations. All these calculations showed that the molecule elongated by ~1 A for polyethylene, but shortened by 0.3–0.5 A for 2,6-octadiene during chain scission. This means that the tensile deformation accelerates the decomposition of polyethylene, but decelerates the decomposition of butadiene rubber.

Consequences of theory level choice evaluated with new tools from QTAIM and the stress tensor for a dipeptide conformer

QTAIM and the stress tensor were used to provide a detailed analysis of the topology of the molecular graph, BCP and bond-path properties, including the new introduced helicity length H, of a Tyr-Gly dipeptide conformer subjected to a torsion with four levels of theory; MP2, M06-2X, B3LYP-D3 and B3LYP and a modest-sized basis set, 6-31+G(d).Structural effects and bonding properties are quantified and reflect differences in the BSSE and lack of inclusion of dispersion effects in the B3LYP calculations. The helicity length H demonstrated that MP2 produced a unique response to the torsion suggesting future use as a diagnostic tool.

Determination of Acidic Dissociation Constants of Chlorthalidone and Terbutaline in Water Using DFT And Ab Initio Methods

I n the present study, pKa values of both drug called Chlorthalidone and Terbutaline were determined in aqueous solution. For this purpose, the B3LYP calculation with the 6-31+G(d) basis set was utilized. The reactions and equilibria that possess a high hydrogen-band-donor capability and constitute the indispensable theoretical basis to calculate the acidity constants of Chlorthalidone and Terbutaline, are shown. To analyze the formation of intermolecular hydrogen bonds between the existent species and water molecules, Tomasi’s method was used. In this way, it was determined that in alkaline aqueous solutions the cation, anion, and neutral species of Chlorthalidone and Terbutaline are solvated with one, two, three, and four molecules of water, respectively. To proceed, the calculated pKa were compared with the experimental values, which there is comparable agreement between them. The resulting data illustrated that the method was likely to be useful for the prediction of pKa values in aqueous solution.

Design of Exceptionally Strong Organic Superbases Based on Aromatic Pnictogen Oxides: Computational DFT Analysis of the Oxygen Basicity in the Gas Phase and Acetonitrile Solution.

DFT B3LYP calculations convincingly showed that aromatic pnictogen oxides offer scaffolds suitable for tailoring powerful organic superbases exhibiting exceptional oxygen basicity in both the gas phase and polar aprotic acetonitrile solution. With their protonation enthalpies and pKa values, they surpass the basicity of classical proton sponges and related nitrogen bases. The most potent system is provided with two arsenic oxide moieties on the phenanthrene framework assisted by the two phosphazeno groups in the para-position to both basic centers. With its proton affinity PA = 300.5 kcal mol-1, the latter system breaks the gas-phase hyperbasicity threshold of 300 kcal mol-1, while its pKa = 54.8 promotes it as an unprecedented superbase in acetonitrile. The origin of such a dramatic basicity enhancement is traced to a fine interplay between (a) steric repulsions of the two negatively charged oxygens destabilizing a neutral base, (b) favorable intramolecular [O-H···O]- hydrogen bonding in conjugate acids, and (c) efficient cationic resonance upon protonation supported by the electron-donating substituents. Given the growing interest in highly basic compounds together with related basic catalysts and metal complexing agents, we hope that the results presented here will open a new avenue of research in these fields and direct attention toward utilizing aromatic pnictogen oxides in designing improved organic materials.

Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer

ABSTRACTB3LYP and MP2 calculations with the commonly-used 6-31+G(d) basis set predict qualitatively different structures for the Tyr–Gly conformer book1, which is the most stable conformer identified in a previous study. The structures differ mainly in the ψtyr Ramachandran angle (138° in the B3LYP structure and 120° in the MP2 structure). The causes for the discrepant structures are attributed to missing dispersion in the B3LYP calculations and large intramolecular BSSE in the MP2 calculations. The correct ψtyr value is estimated to be 130°. The MP2/6-31+G(d) profile identified an additional conformer, not present on the B3LYP surface, with a ψtyr value of 96° and a more folded structure. This minimum is, however, likely an artefact of large intramolecular BSSE values. We recommend the use of basis sets of at least quadruple-zeta quality in density functional theory (DFT), DFTaugmented with an empirical dispersion term (DFT-D) and second-order Møller-Plesset perturbation theory (MP2 ) calculations in cases where intramolecular BSSE is expected to be large.

Performance of different density functionals for the calculation of vibrational frequencies with vibrational coupled cluster method in bosonic representation

An accurate description of anharmonic vibrational frequencies of polyatomic molecules is a challenging task. It requires an ab initio method to solve the vibrational Schrodinger equation along with extensive electronic structure calculations to generate the quartic potential energy surface (PES) in mass-weighted normal coordinates. The computation of such quartic PES is very expensive. Even for a medium-size molecule, highly accurate ab initio methods like CCSD, CCSD(T) become formidable. The DFT stands as valuable alternative in this case. In this work, we investigate the performances of several commonly used density functionals, namely, B3LYP, BLYP, B3LYPD, M06, M062x, PBE1PBE, B3P86, LC- $$\omega $$ PBE, X3LYP, B3PW91, and B97D for the evaluation of anharmonic vibrational frequencies of semi-rigid molecules. The quality of the results is assessed by the comparison with experimental values. To this end, we used a set of 19 molecules of various sizes (4–9 atoms). The vibrational coupled cluster method (VCCM) in bosonic representation is used to solve the vibrational structure problem. The hybrid functionals B3P86, B3LYP, B3PW91, PBE1PBE, and X3LYP found to give more accurate result of the fundamental frequencies than the other functionals. Our results show that the error in the BLYP and B97D calculation is due to the inadequate description of the harmonic force field. For the LC- $$\omega $$ PBE, M06, and M062x, the anharmonic force constants leads to the error. It is found that the comparative performances of the DFT functionals with VCCM are consistent with the second-order vibrational perturbation theory.

Matrix-isolation infrared spectrum of acenaphthene in the lowest electronically excited triplet (T1) state

Since acenaphthene isolated in an Ar matrix at 15 K emits green-yellow phosphorescence for ∼10 s after stopping UV-light irradiation, its transient IR spectrum is expected to be measured with an FTIR spectrometer during UV irradiation. The transient spectrum observed is found to be consistent with the simulated spectrum of acenaphthene in the lowest electronically excited triplet (T1) state calculated at the B3LYP/6–31++G(d,p) level. The spectral pattern obtained using the B3LYP functional, which is the most popular DFT hybrid functional, reproduces the observed spectrum more satisfactorily than that obtained using the recently proposed M06-2x functional, although the optimized geometrical parameters in the both calculations are not so different from each other. The IR-band assignments of the T1 state and the structural changes from the S0 state to the T1 state are discussed based on the results of B3LYP calculation.

Experimental and computational thermochemical studies of acridone and N-methylacridone

Abstract This paper reports the standard (p° = 0.1 MPa) molar enthalpies of formation, in the gaseous phase, at T = 298.15 K, of acridone and N-methylacridone as (50.0 ± 5.0) kJ·mol−1 and (60.6 ± 4.3) kJ·mol−1, respectively. These data were obtained from experimental thermodynamic parameters, namely the standard molar enthalpies of formation, in the crystalline phase, at T = 298.15 K, derived from the standard molar enthalpies of combustion measured by static-bomb combustion calorimetry, and the standard molar enthalpies of sublimation, at T = 298.15 K, determined by Calvet microcalorimetry or the Knudsen effusion techniques. Additionally, the gas-phase enthalpies of formation were estimated by G3(MP2)//B3LYP calculations, using several hypothetical gas-phase reactions, and were compared with the corresponding ones determined experimentally. The gas-phase keto-enol tautomerization chemical equilibrium of acridone ↔ 9-acridinol was analysed using the Boltzmann’s distribution, being confirmed that the equilibrium favours the formation of the keto form. The bond dissociation enthalpies (N-H) and (C-H) and the gas-phase acidities were also determined. The electrostatic potential surfaces and the frontier molecular orbitals were determined for both compounds, allowing us to infer about their reactivity properties. Other properties studied include the HOMO-LUMO energy gap and the ionization potential.

Evaluation of the structural properties of powerful pesticide dieldrin in different media and their complete vibrational assignment

Dieldrin was characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman), Ultraviolet–Visible (UV–Visible) spectroscopies. The structural and vibrational properties for dieldrin in gas phase and in aqueous solution were computed combining those experimental spectra with hybrids B3LYP and WB97XD calculations by using the 6-31G* and 6-311++G** basis sets. Here, the experimental available Hydrogen and Carbon Nuclear Magnetic Resonance (1H and 13C NMR) for dieldrin were also used and compared with those predicted by calculations. The B3LYP/6-311++G** method generates the most stable structures while the results have demonstrated certain dependence of the volume and dipole moment values with the method, size of the basis set and, with the studied media. The lower solvation energy for dieldrin (−32.94 kJ/mol) is observed for the higher contraction volume (−2.4 Å3) by using the B3LYP/6-31G* method. The NBO studies suggest a high stability of dieldrin in gas phase by using the WB97XD/6-31G* method due to the n→π* and n*→π* interactions while the AIM analyses support this high stability by the C18⋯H26 and C14⋯O7 contacts. The different topological properties observed in the R5 ring suggest that probably this ring plays a very important role in the toxics properties of dieldrin. The frontier orbitals show that when dieldrin is compared with other toxics substances the reactivity increases in the following order: CO < STX < dieldrin < C6Cl6 <TCAB < TCAOB < CN− where evidently, the presence of five rings and six Cl atoms decrease the reactivity of dieldrin, as compared with hexachlorobencene. The WB97XD method and the two basis sets predicted for dieldrin in both media low reactivities, higher nucleophilicity and, low electrophilicity. All the bands observed in the IR and Raman spectra were completely assigned to the 75 vibration normal modes and their harmonic force fields and force constants for first time are reported for dieldrin. The predicted FTIR, FT-Raman, UV–Visible and 1H and 13C NMR spectra for dieldrin show a reasonable concordance with the experimental ones.

Alkalized borazine: A simple recipe to design closed‐shell superalkalis

AbstractSuperalkalis are hypervalent species, possessing smaller ionization energy (IE) than alkali metal. These species are typically designed by electronegative atoms with excess electropositive ligands. Typical examples include FLi2, OLi3, NLi4, etc. Herein, we study successive alkali metal substitution at H atoms in borazine (B3N3H6). Our B3LYP and MP2 calculations demonstrate that the vertical ionization energy (VIE) of B3N3H6‐xLix decreases with the increase in x for x = 1–6. For x ≥ 4, the VIE of B3N3H6‐xLix becomes lower than that of Li atom, thereby indicating their superalkali nature. More interestingly, all these species are planar with closed‐shell structure such that the NICSzz value at the ring's center is reduced. We have also studied B3N3M6 (M = Li, Na, and K) species and found that the VIE is further reduced in case of Na and K substitutions. These findings should suggest a simple yet effective route to the design of species with lower ionization energies than alkali metal.

Synthesis and characterization of p-xylylenediaminium bis(nitrate). Effects of the coordination modes of nitrate groups on their structural and vibrational properties

The p-xylylenediaminium bis(nitrate) compound have been synthesized and then, it was characterized by using Fourier Transform infrared (FT-IR) in the solid phase and, by using the Ultraviolet–Visible (UV–Visible) and Hydrogen and Carbon Nuclear Magnetic Resonance (1H- and 13C-NMR) spectra in aqueous solution and in dimethylsulfoxide solvent. In this work, two monodentate and bidentate coordination modes were considered for the nitrate ligands in both media in order to study the structural and vibrational properties of that salt. Hence, the natural bond orbital (NBO), atoms in molecules (AIM), Merz-Kollman (MK) charges, molecular electrostatic potentials (MEP) and frontier orbitals studies were performed for p-xylylenediaminium bis(nitrate) and their cation and anion species taking into account for the salt those two coordination modes for the nitrate ligands. The intermolecular interactions of this salt were also evaluated by Hirshfeld surface analysis. The B3LYP calculations performed by using the hybrid method and the 6-311G* and 6-311++G** basis sets generate monodentate and bidentate structures with Ci and C2 symmetries, respectively. The force fields and the force constants values for these two structures were also computed and their complete vibrational assignments were performed by using those both levels of theory. The strong band at 1536 cm−1, the bands between 2754 and 2547 cm−1 and the bands between 1779 and 1704 cm−1 support clearly the presence of the dimeric species while the IR bands at 1986/1856 cm−1 could justify the presence of the bidentate species in the solid phase.

The insertion and H2 elimination reactions of H2GeFMgF germylenoid with RH (R = Cl, SH, PH2)

In present paper, the insertion and H2 elimination reactions of H2GeFMgF germylenoid with RH (R = Cl, SH, PH2) were investigated by means of B3LYP and QCISD calculation methods. One transition state and one intermediate were found along the potential energy surface in each insertion reaction, while for the H2 elimination reactions, only one transition state was found between the reactants and products in each reaction process. Both for the insertion and H2 elimination reactions, RH reactivity increases in the following order: H–Cl > H–SH > H–PH2. The insertion and H2 elimination reactions were compared, and the results demonstrated that the H2 elimination should be more favorable than the corresponding insertion. The solvent effects on these two types of reactions were considered. The calculated results indicated that the solvents could accelerate the reactions by reducing their barrier heights.

Tautomerism of N-(3,4-dichlorophenyl)-1H-indazole-5-carboxamide – A new selective, highly potent and reversible MAO-B inhibitor

The tautomeric properties of an N-(3,4-dichlorophenyl)-1H-indazole-5-carboxamide (NTZ-1006, 2) derivative, developed as highly potent, reversible and selective MAO-B inhibitor useful for the treatment of Parkinson's disease (PD) and other neurological disorders, have been studied both experimentally and theoretically. The theoretical data (M06–2X, B3LYP and MP2-4 quantum chemical calculations) have shown that due to aromaticity reasons the 1H tautomer strongly dominates over the 2H form. There are no substantial spectral changes by changing the solvent and the concentration, which leads to a conclusion that compound 2 exists in solution as 1H tautomer and its tautomerism is not influenced by the solvents and the concentration. The results are in line with the understanding for the tautomerism of 1H-indazole and shows that substitution at the C5 position in the indazole unit does not influence the tautomeric state.The isolated crystal structure of 2 is in an excellent agreement with the computation in respect of the most stable tautomer. Combined single X-ray/molecular modeling studies including HYdrogen-DEsolvation (HYDE) analysis provided not only insights into the enzyme–inhibitor interaction within the binding site of the human MAO-B isoform, but also a valuable information regarding the most stable 1H-indazole tautomeric form of NTZ-1006 that contributes to its high potency against hMAO-B enzyme (IC50 0.586 nm) and selectivity (>17000-fold) over the hMAO-A isoenzyme.

On NMR prediction of the antioxidant effectiveness of heterocyclic nitrogen compounds and substituted amines in styrene-butadiene rubber

Structures of 13 heterocyclic nitrogen compounds and substituted tertiary amines were optimized and their NMR shifts were evaluated by B3LYP calculations. The relation between experimental values of Molar Antioxidant Effectiveness (AEM) in styrene-butadiene rubber at various temperatures and calculated NMR chemical shifts of nitrogens and hydrogens bonded to them was investigated. AEM values are negatively affected by additional non-nitrogen heteroatoms. Only the molecules containing nitrogen atoms with NMR chemical shifts under −277 ppm are usable as antioxidants.

Second–shell thermochemistry for hydration of strontium dications as determined by threshold collision-induced dissociation and computations

This work reports a continuation of the guided ion beam tandem mass spectrometer (GIBMS) study of the threshold collision-induced dissociation of Sr2+(H2O)x. The present study measures 0K hydration energies for Sr2+(H2O)x, where x=7–9, which can be added to those previously measured for x=1–6. The full range of these complexes is also examined theoretically employing B3LYP/SDD/def2-TZVP and B3LYP/DHF/def2-TZVPP geometry optimizations with additional B3LYP, B3P86, M06, and MP2(full) single point energy calculations performed with the larger SDD/def2-TZVPP and DHF/def2-TZVPP basis sets, respectively. The transition between first and second hydration shells is explored from both experimental and theoretical findings. Neither experimental nor theoretical results are completely consistent with a single coordination number for the first hydration shell at 298K, but rather suggest mixed coordination numbers ranging from 6 to 8 water molecules.

Theoretical spectroscopic insights of tautomers and enantiomers of penicillamine

B3LYP and MP2 calculations have been carried out to investigate tautomers and enantiomers of penicillamine (Pen). Their infrared (IR), ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectra were obtained at linear-response, time-dependent DFT (TD-DFT). IR, UV and NMR spectra cannot be used to identify Pen enantiomers, showing nearly equal spectral profiles. CD spectra, however, give rise to completely symmetric signals, forming a perfect specular image to each other. Distinct CD profiles were also obtained for Pen tautomers. Important IR differences were found in positions and intensities of the vibrational stretching bands involving acid and amine groups of Pen tautomers. The highest electron transitions involving HOMO-LUMO orbitals show to be of major importance in the computed UV spectra, showing a large red-shift around 30nm as the zwitterionic and neutral Pen spectra are compared. NMR results show to be quite useful for identification of Pen tautomers since clear differences are found by means of the computed shielding tensors as well as spin-spin coupling constants 1J(N,H) data.

Prediction of neutral noble gas compounds LiNgF (Ng = Kr, Xe and Rn)

The structure and stability of LiNgF (Ng=Kr, Xe and Rn) molecules were investigated by using B3LYP, MP2 and CCSD(T) calculations. The theoretical results indicate that LiKrF is an unstable compound due to possessing two small negative frequencies, but LiXeF and LiRnF species are thermochemically stable with respect to their “three-body” dissociated products Li+Ng+F, and kinetically stable with respect to their “two-body” dissociated products Ng+LiF. The bonding nature of noble-gas atoms in LiXeF and LiRnF was also analyzed by using the quantum theory of atoms in molecules (QTAIM) approach and natural bond orbital (NBO) analysis.

Theoretical Study of the Kinetics and Mechanism of the Thermal Decomposition of 3-Oxetanone in the Gas Phase

The kinetics and mechanism of the thermal decomposition reaction of 3-oxetanone in the gas phase were studied using quantum chemical calculations. The major products of this reaction are formaldehyde, ketene, carbon monoxide, ethylene oxide, ethylene and methyl radical. Formaldehyde, ketene, carbon monoxide and ethylene oxide are the initial decomposition products and other species are the products of ethylene oxide decomposition. The results of B3LYP and QCISD(T) calculations reveal that thermal decomposition of 3-oxetanone to ethylene oxide and carbon monoxide is more probable than to formaldehyde and ketene from an energy viewpoint. Moreover, quantum theory of atoms in molecules and natural bond orbital analysis indicate that 3-oxetanone decomposition to formaldehyde, ketene, carbon monoxide and ethylene occurs via a concerted mechanism and bonds that are involved in the transition states have a covalent character. Moreover, the calculated changes in bond lengths in the transition states reveal that bond breaking and new bond formation occur asynchronously in a concerted mechanism.

2-巯基吡啶配合物的合成及量子化学计算

基于配体2,2’-二硫二吡啶(简称Dpds)，采用分层扩散法，合成出六核簇状配位化合物Cu6(C5H4NS)6。采用密度泛函理论(DFT)下的B3LYP计算方法、NBO计算方法对该配合物进行量子化学计算，同时进行了前线轨道的研究。结果表明：每个配合物含六个铜离子、六个2-巯基吡啶阴离子，优化后的理论值与实验值比较吻合，误差在允许的范围内，理论计算的完成证明了实验数据的可靠性。 A six-core cluster compound Cu6(C5H4NS)6, was prepared by layered a N, N-Dimethylformamide solution of Cu(CH3COO)2•H2O on a dichloromethane solution of Dpds. The quantum chemistry cal-culation of the complex was carried out by using the B3LYP calculation method of density functional theory (DFT) and the NBO calculation method; at the same time, the research of frontier orbital is carried out. The results showed that the six-core copper (II) cluster complex contains six crystallographically unique Cu (II) ions and six 2-mercapto pyridine anions. It is found that the theoretical values are in agreement with the experimental ones, and the error is within the al-lowable range. And the completion of theoretical calculations proved the reliability of the experi-mental data.

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH–, nH2O/OH–, nH2O (where n = 1, 2, 3), and protonated melamine with H2O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6-31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6-31G(d), 6-31 + G(d), 6-31G(2df,p), and 6-311++G(3df,3pd). B3LYP, M06, and ωB97XD calculations with 6-31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6-31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS-QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3-proton shift. The lowest overall activation energy, 111 kJ mol−1 at G4MP2, was obtained for the deamination of melamine with 3H2O/OH−.