Structure and electronic properties of azadirachtin

We performed a combined DFT and Monte Carlo ¹³C NMR chemical-shift study of azadirachtin A, a triterpenoid that acts as a natural insect antifeedant. A conformational search using a Monte Carlo technique based on the RM1 semiempirical method was carried out in order to establish its preferred structure. The B3LYP/6-311++G(d,p), wB97XD/6-311++G(d,p), M06/6-311++G(d,p), M06-2X/6-311++G(d,p), and CAM-B3LYP/6-311++G(d,p) levels of theory were used to predict NMR chemical shifts. A Monte Carlo population-weighted average spectrum was produced based on the predicted Boltzmann contributions. In general, good agreement between experimental and theoretical data was obtained using both methods, and the ¹³C NMR chemical shifts were predicted highly accurately. The geometry was optimized at the semiempirical level and used to calculate the NMR chemical shifts at the DFT level, and these shifts showed only minor deviations from those obtained following structural optimization at the DFT level, and incurred a much lower computational cost. The theoretical ultraviolet spectrum showed a maximum absorption peak that was mainly contributed by the tiglate group.     

Comparative theoretical study of the UV/Vis absorption spectra of styrylpyridine compounds using TD-DFT calculations

This study examined absorption properties of 2-styrylpyridine, trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)]pyridine, and trans-4-(m-cyanostyryl)pyridine compounds based on theoretical UV/Vis spectra, with comparisons between time-dependent density functional theory (TD-DFT) using B3LYP, PBE0, and LC-ωPBE functionals. Basis sets 6–31G(d), 6–31G(d,p), 6–31+G(d,p), and 6–311+G(d,p) were tested to compare molecular orbital energy values, gap energies, and maxima absorption wavelengths. UV/Vis spectra were calculated from fully optimized geometry in B3LYP/6–311+G(d,p) in gas phase and using the IEFPCM model. B3LYP/6–311+G(d,p) provided the most stable form, a planar structure with parameters close to 2-styrylpyridine X-ray data. Isomeric structures were evaluated by full geometry optimization using the same theory level. Similar energetic values were found: ～4.5 kJ?mol^?1 for 2-styrylpyridine and ～1 kJ?mol^?1 for derivative compound isomers. The 2-styrylpyridine isomeric structure differed at the pyridine group N-atom position; structures considered for the other compounds had the cyano group attached to the phenyl ring m-position equivalent. The energy difference was almost negligible between m-cyano-substituted molecules, but high energy barriers existed for cyano-substituted phenyl ring torsion. TD-DFT appeared to be robust and accurate approach. The B3LYP functional with the 6–31G(d) basis set produced the most reliable λ_max values, with mean errors of 0.5 and 12 nm respect to experimental values, in gas and solution, respectively. The present data describes effects on the λ_max changes in the UV/Vis absorption spectra of the electron acceptor cyano substituent on the phenyl ring, the electron donor methyl substituent, and the N-atom position on the electron acceptor pyridine ring, causing slight changes respect to the 2-styrylpyridine title compound.     

Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes

This paper presents an ab initio quantum chemical investigation of the geometrical structures and the non-linear optical properties (NLO) of three structural isomers of pyridinium N-phenolate betaine dye. The ground state geometrical parameters and the first-order hyperpolarizabilities were calculated using the Hartree-Fock (HF) as well as the second-order perturbation Møller-Pleset (MP2) method with the 6–31G, 6–31G(d), 6–31G(d,p), 6–31+G(d), 6–31++G(d,p), 6–311+G(d), aug-cc-PVDZ and the recently developed Z3PolX basis sets. Moreover, the first-order hyperpolarizability was calculated at the coupled cluster singles and doubles (CCSD/6–31+G(d)) level of theory. The analysis of the results of calculations for the investigated isomers indicates that there are important differences in their NLO activities. Additionally, it was shown that Z3PolX basis set works reasonable well for betaine dyes.

Density functional theory investigation of electrophilic addition reaction of bromine to tricyclo[4.2.2.22,5]dodeca-1,5-diene1

The geometry and the electronic structure of tricyclo[4.2.2.2^2,5]dodeca-1,5-diene (TCDD) molecule were investigated by DFT/B3LYP and /B3PW91 methods using the 6-311G(d,p) and 6-311++G(d,p) basis sets. The double bonds of TCDD molecule are syn-pyramidalized. The structure of π-orbitals and their mutual interactions for TCDD molecule were investigated. Potential energy surface (PES) of the TCDD-Br₂ system was studied by B3LYP/6-311++G(d,p) method and the configurations [molecular charge-transfer (CT) complex, transition states (TS1 and TS2), intermediate (INT) and product (P)] corresponding to the stationary points (minima or saddle points) were determined. Initially, a molecular CT-complex forms between Br₂ and TCDD. With a barrier of 22.336 kcal mol^-1 the CT-complex can be activated to an intermediate (INT) with energy 15.154 kcal mol^-1 higher than that of the CT-complex. The intermediate (INT) then transforms easily (barrier 5.442 kcal mol^-1) into the final, N-type product. The total bromination is slightly exothermic. Accompanying the breaking of Br-Br bond, C1-Br, C5-Br and C2-C6 bonds are formed, and C1 = C2 and C5 = C6 double bonds transform into single bonds. The direction of the reaction is determined by the direction of intramolecular skeletal rearrangement that is realized by the formation of C2-C6 bond.

Reaction mechanism of CH3M≡MCH3 (M=C, Si, Ge) with C2H4: [2+1] or [2+2] cycloaddition?

The mechanism of the cycloaddition reaction CH₃M≡MCH₃ (M=C, Si, Ge) with C₂H₄ has been studied at the CCSD(T)/6-311++G(d,p)//MP2/6-311++G(d,p) level. Vibrational analysis and intrinsic reaction coordinate (IRC), calculated at the same level, have been applied to validate the connection of the stationary points. The breakage and formation of the chemical bonds of the titled reactions are discussed by the topological analysis of electron density. The calculated results show that, of the three titled reactions, the CH₃Si≡SiCH₃+C₂H₄ reaction has the highest reaction activity because it has the lowest energy barriers and the products with the lowest energy. The CH₃C≡CCH₃+C₂H₄ reaction occurs only with difficulty since it has the highest energy barriers. The reaction mechanisms of the title reactions are similar. A three-membered-ring is initially formed, and then it changed to a four-membered-ring structure. This means that these reactions involve a [2+1] cycloaddition as the initial step, instead of a direct [2+2] cycloaddition.     

Density functional theory characterisation of 4-hydroxyazobenzene

We report the structural properties, infrared (IR) and Raman spectra, dipole moment, polarisability, hardness and chemical potential of the trans and cis configurations of 4-hydroxyazobenzene calculated using the B3LYP functionals. All calculations were performed with the following basis sets: 6–31G, 6–31++G, 6–31G(d,p), 6–31++G(d,p), 6–31G(2d,2p), 6–31++G(2d,2p) and 6–311++G(2d,2p). We observed that 6–31++G(d,p) gives similar results to 6–311++G(2d,2p). Consequently, SVWN and PW91 methods were also used in association with 6–31++G(d,p) to test the influence of the different models of exchange and correlation functionals. A planar structure was obtained for all the optimised trans configuration structures. In both isomers, the presence of the hydroxyl group leads to an asymmetry in certain structural parameters. From these results, two IR or Raman active frequencies can be used to easily distinguish trans and cis configurations. The trans configuration was found to be more stable than the cis configuration by 67 ± 2 kJ mol⁻¹ at 0 K. The difference of the dipole moment between trans and cis for 4-hydroxyazobenzene was found to be lower than for trans and cis azobenzene.     

Studies on molecular structure and tautomerism of a vitamin B<Subscript>6</Subscript> analog with density functional theory

This work presents a computational study on the molecular structure and tautomeric equilibria of a novel Schiff base L derived from pyridoxal (PL) and o-phenylenediamine by using the density functional method B3LYP with basis sets 6-31 G(d,p), 6-31++G(d,p), 6-311 G(d,p) and 6-311++G(d,p). The optimized geometrical parameters obtained by B3LYP/6-31 G(d,p) method showed the best agreement with the experimental values. Tautomeric stability study of L inferred that the enolimine form is more stable than its ketoenamine form in both gas phase and solution. However, protonation of the pyridoxal nitrogen atom (LH) have accelerated the formation of ketoenamine form, and therefore, both ketoenamine and enolimine forms could be present in acidic media.     

A dynamics prediction of nitromethane → methyl nitrite isomerization in external electric field

As a follow-up to our investigation into the effect of external electric field on the chemical bond strength, the effects of external electric field on the CH₃NO₂ → CH₃ONO isomerization dynamics were investigated using the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p) methods. The rate constants in the absence and presence of various field strengths were calculated. The results show that, when the field strength is larger than +0.0060 a.u. along the C?NO₂ bond axis, the barriers of the isomerization are lower than the C–NO₂ bond dissociation energies, leading to the preferences of the isomerization over the C?NO₂ bond dissociation. In this case, the sensitivities are higher than that in no field. However, in the other fields, the C–NO₂ bond scission is favored and the sensitivities are almost equal to that in no field. Several good linear correlations are found between the field strengths and the changes of the bond lengths or corresponding electron densities.     

MP2, density functional theory, and molecular mechanical calculations of C-H···π and hydrogen bond interactions in a cellulose-binding module-cellulose model system

Exploring non-covalent interactions, such as C-H···π stacking and classical hydrogen bonding (H-bonding), between carbohydrates and carbohydrate-binding modules (CBMs) is an important task in glycobiology. The present study focuses on intermolecular interactions, such as C-H?π (sugar-aromatic stacking) and H-bonds, between methyl β-d-glucopyranoside and l-tyrosine—a proxy model system for a cellulose-CBM complex. This work has made use of various types of quantum mechanics (QM) and molecular mechanics (MM) methods to determine which is the most accurate and computationally efficient. The calculated interaction potential energies ranged between −24 and −38 kJ/mol. The larger interaction energy is due to H-bonding between the phenyl hydroxyl of tyrosine and the O4 of the sugar. Density functional theory (DFT) methods, such as BHandHLYP and B3LYP, exaggerate the H-bond. Although one of the MM methods (viz. MM+) considered in this study does maintain the C-H?π stacking configuration, it underestimates the interaction energy due to the loss of the H-bond. When the O-H bond vector is in the vicinity of O4 (O-H?O4 ≈ 2 Å, e.g., in the case of MP2/6-31G(d)), the torsional energy drops to a minimum. For this configuration, natural bond orbital (NBO) analysis also supports the presence of this H-bond which arises due to orbital interaction between one lone pair of the sugar O4 and the σ∗(O-H) orbital of the phenyl group of tyrosine. The stabilization energy due to orbital delocalization of the H-bonded system is ∼13 kJ/mol. This H-bond interaction plays an important role in controlling the CH/π interaction geometry. Therefore, the C-H?π dispersive interaction is the secondary force, which supports the stabilization of the complex. The meta-hybrid DFT method, M05-2X, with the 6-311++G(d,p) basis set agrees well with the MP2 results and is less computationally expensive. However, the M05-2X method is strongly basis set dependent in describing this CH/π interaction. Computed IR spectra with the MP2/6-31G(d) method show blue shifts for C1-H, C3-H, and C5-H stretching frequencies due to the C-H?π interaction. However, the M05-2X/6-311++G(d,p) method shows a small red shift for the C1-H stretching region and blue shifts for the C2-H and C3-H stretches. For the aromatic tyrosine C_δ1-C_ε1 and C_δ2-C_ε2 bonds in the complex, the calculated IR spectra show red shifts of 12 cm⁻¹ (MP2/6-31G(d)) and 5 cm⁻¹ (M05-2X/6-311++G(d,p)). This study also reports the upfield shifts of computed ¹H NMR chemical shifts due to the C-H?π interaction.     

The Hydronium Tetrafluoroborate Dimer in Nonpolar Media and its Proton NMR Spectrum

Hydronium tetrafluoroborate ion pairs, H₃O⁺·BF₄ ^- have been shown computationally to be unstable toward decomposition, in the absence of solvation or electrostatic interactions existing in crystals. As the proton NMR spectrum of a hydronium salt with the octanesulfonate-antimony pentachloride complex anion was reported in freon solution, we investigated the hypothesis that larger ionic clusters were present in the nonpolar solvent. It was found that the dimer (H₃O⁺·BF₄ ^-)₂ was stable at the MP2/6-31G* level. GIAO-B3LYP chemical shift calculations with the same basis set and also with the 6-31G**, 6-31++G**, 6-311++G**, dzvp, tzp, tz2p, and qz2p basis sets conducted on the hydronium fluoroborate dimer reproduce the main features of the experimental spectrum: the existence of two signals with a two-to-one intensity ratio and the more intense resonance at higher frequency (more deshielded). The alternative structures, of hydronium tetrafluoroborate ion pairs with one and with two hydrogen bonds between anion and cation, give calculated chemical shifts which are farther from the experimental values.     

Computational Study of the Sulfonylated Amino Acid Hydroxamates Binding to the Zinc Ion within the Active Site of Carbonic Anhydrase

Abstract

The B3LYP/6–311+G(d,p) method and three ONIOM extrapolation methods ONI-OM (B3LYP/6–311+G(d,p): AM1); ONIOM(B3LYP/6–311+G(d,p): MNDO); ONIOM (B3LYP/6–311+G(d,p): HF/3-21G(d)) were used to characterize the complexes of Zn²⁺ cation with anionic sulfonylated amino acid hydroxamates (RSO₂NH-AA-CON(-)OH), possessing an unsubstituted RSO₂NH—amino acyl moiety. According to the R moiety we distinguish between pentafluorophenyl and 4-methoxyphenyl derivates. The amino acid hydroxamates included in the study were the Gly, Ala, and Leu derivates. Of the inhibitors investigated, the weakest zinc affinity exhibits the pentafluorophenyl derivate with Gly amino acid and the strongest affinity the 4-methoxyphenyl derivate with Leu amino acid. The inhibitors form bidentate coordination bonds with the zinc cation by means of the sulfonyl oxygen and the ionized hydroxamate nitrogen atoms, respectively. The zinc affinities computed using the B3LYP/6–311 +G(d,p)//HF/6–31 +G(d,p) method are in very good agreement with the full density functional theory (DFT) B3LYP/6–311+G(d,p)//B3LYP/6- 311+G(d,p) method and this method can be adopted to model larger complexes of inhibitors with the active site of carbonic anhydrase.     

Theoretical Ab initio study of the effects of methylation on the nature of hydrogen bonding in A:T base pair

We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6-31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.     

Theoretical ab initio study of the effects of methylation on structure and stability of G:C Watson-Crick base pair

Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries of the local minima were optimized without symmetry restrictions by the gradient procedure at DFT level of theory and were verified by energy second derivative calculations. The standard 6-31G(d) basis set was used. The single-point calculations have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stability and counterpoise corrected interaction energies are reported. Also, using a variation-perturbation energy decomposition scheme we have found the vital contributions to the total interaction energy.     

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the molecule-cation interaction between Na⁺ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO₂ bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO₂ bond upon complex formation, leading to the strengthened C-NO₂ bond and the possibly reduced explosive sensitivity.

Exploration of various electronic properties along the reaction coordinate for hydration of Pt(II) and Ru(II) complexes; the CCSD, MPx, and DFT computational study

In the study behavior of molecular electrostatic potential, averaged local ionization energy, and reaction electronic flux along the reaction coordinate of hydration process of three representative Ru(II) and Pt(II) complexes were explored using both post-HF and DFT quantum chemical approximations. Previously determined reaction mechanisms were explored by more detailed insight into changes of electronic properties using ωB97XD functional and MP2 method with 6–311++G(2df,2pd) basis set and CCSD/6–31(+)G(d,p) approach. The dependences of all examined properties on reaction coordinate give more detailed understanding of the hydration process.

Racemization of the gastrointestinal antisecretory chiral drug esomeprazole magnesium via the pyramidal inversion mechanism: A theoretical study

The pyramidal inversion mechanisms of the 6‐methoxy and the 5‐methoxy tautomers of (S)‐omeprazole were studied, employing ab initio and DFT methods. The conformational space of the model molecule (S)‐2‐[(3‐methyl‐2‐pyridinyl)methyl]sulfinyl‐1H‐benzimidazole was calculated, with respect to rotations around single bonds, at the B3LYP/6‐311G(d,p) level. All of the resulting conformations were used as starting points for full optimizations of (S)‐omeprazole, at B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), B3LYP/6‐311++G(d,p), B3LYP/6‐311G(2df,2pd), MP2/6‐31G(d), and MP2/6‐311G(d,p) levels. Four distinct pathways were found for enantiomerization via the pyramidal inversion mechanism for each of the tautomers of (S)‐omeprazole. Each transition state, in which the sulfur, the oxygen and the two carbon atoms connected directly to the sulfur are in one plane, connects two diastereomeric minima. The enantiomerization is completed by free rotation around the sulfur–methylene bond, and around the methylene–pyridine ring bond. The effective Gibbs' free energy barrier for racemization ΔG of the two tautomers of (S)‐omeprazole are 39.8 kcal/mol (5‐methoxy tautomer) and 40.0 kcal/mol (6‐methoxy tautomer), indicating that the enantiomers of omeprazole are stable at room temperature (in the gas phase). The 5‐methoxy tautomer of (S)‐omeprazole was found to be slightly more stable than the 6‐methoxy tautomer, in the gas phase. The energy barrier (ΔG^?) for the(S,M) (S,P) diastereomerization of (S)‐omeprazole due to the rotation around the pyridine chiral axis was very low, 5.8 kcal/mole at B3LYP/6‐311G(d,p). Chirality 2010. © 2010 Wiley‐Liss, Inc.     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

The (α-1,6) glycosidic bond of isomaltose: a tricky system for theoretical conformational studies

Stable conformations of β-isomaltose (α-d-glucopyranosyl-(1→6)-β-d-glucose) in gas-phase and aqueous solution are investigated in this study using quantum mechanical calculations. Conformational maps are calculated at HF/6-31G(d,p) level and lower energy structures are sampled in the most stable regions. Entropic and thermal corrections are considered and the Boltzmann population is obtained for conformers that are representative of the 18 most stable regions found on the potential energy surface. B3LYP/6-31+G(d,p) and B3LYP/6-311+G(2d,2p) calculations are used in conformational samplings. Solvation effects are considered through the polarizable continuum model approach. Hydroxymethyl group orientations are investigated for the most stable conformers. The influence of electronic correlation and solvation on the glycosidic linkage preference (TG, GT, and GG) and hydroxymethyl group orientation (tg, gt, and gg) are discussed. Heteronuclear spin coupling constants (³J_C,H) along the glycosidic linkage are calculated and comparison with other theoretical results and experiments is used to validate the obtained structures.