Conformational equilibrium study of calix[4]tetrolarenes using Density Functional Theory (DFT) and Molecular Dynamics simulations

The present work deals with the theoretical study of conformational equilibrium of calix[4]tetrolarenes (1,2,3 trimethoxy substituted calix[4]arene) in gaseous and solvation phases. A total of 64 calculations (four conformations at eight level of theories) were performed using Density Functional Theory (DFT) functionals viz. wB97XD, B97D, B3LYP, CAM-B3LYP with diffused (6–31 + G(d)) and non-diffused basis sets (6-31G(d)). It has been found that the conformational profile of calix[4]tetrolarene changes from cone to 1,3-Alternate upon incorporating – OMe group. The B97D and wB97XD functionals gave the most accurate result having rmsd value ~0.73Å followed by B3LYP and CAM-B3LYP > 0.78Å. Furthermore, NBO calculations demonstrated that reduction in charges at lower rim oxygens reduces the chances of hydrogen bonding. Moreover, global reactivity parameters and molecular dynamics also complement the observed trend. Owing to the methoxy substitutions, anion binding study of these new molecules indicates towards the promising capability to bind Cl^? and F^? ions.     

DFT calculations on the catalytic oxidation of CO over Si-doped (6,0) boron nitride nanotubes

The oxidation of carbon monoxide (CO) is important for a series of technological and environmental applications. In this work, the catalytic oxidation of CO on Si-doped (6,0) boron nitride nanotubes (BNNTs) is investigated by using density functional theory calculations. Reaction barriers and corresponding thermodynamic parameters were calculated using the M06-2X, B3LYP and wB97XD density functionals with 6-31G* basis set. Our results indicate that a vacancy defect in BNNT strongly stabilizes the Si adatom and makes it more positively charged. This charging enhances the adsorption of reaction gases (O₂ and CO) and results in the change of the electronic structure properties of the tube. The calculated barrier of the reaction CO + O₂ → CO₂ + O_ads on Si-doped BNNTs following the Langmuir–Hinshelwood is lower than that on the traditional noble metal catalysts. The second step of the oxidation would be the Eley–Rideal reaction (CO + O_ads → CO₂) with an energy barrier of about 1.8 and 10.1 kcal/mol at M06-2X/6-31G* level. This suggests that the CO oxidation catalyzed by the Si-doped BNNTs is likely to occur at the room temperature. The results also demonstrate that the activation energies and thermodynamic quantities calculated by M06-2X, B3LYP and wB97XD functionals are consistent with each other.     

Theoretical Modelling of Photoswitching of Hyperpolarisabilities in Ruthenium Complexes

Static excited‐state polarisabilities and hyperpolarisabilities of three Ru^II ammine complexes are computed at the density functional theory (DFT) and several correlated ab initio levels. Most accurate modelling of the low energy electronic absorption spectrum is obtained with the hybrid functionals B3LYP, B3P86 or M06 for the complex [Ru^II(NH₃)₅(MeQ⁺)]³⁺ (MeQ⁺=N‐methyl‐4,4′‐bipyridinium, 3 ) in acetonitrile. The match with experimental data is less good for [Ru^II(NH₃)₅L]³⁺ (L=N‐methylpyrazinium, 2 ; N‐methyl‐4‐{E,E‐4‐(4‐pyridyl)buta‐1,3‐dienyl}pyridinium, 4 ). These calculations confirm that the first dipole‐ allowed excited state (FDAES) has metal‐to‐ligand charge‐transfer (MLCT) character. Both the solution and gas‐phase results obtained for 3 by using B3LYP, B3P86 or M06 are very similar to those from restricted active‐space SCF second‐order perturbation theory (RASPT2) with a very large basis set and large active space. However, the time‐dependent DFT λ_max predictions from the long‐range corrected functionals CAM‐B3LYP, LC‐ωPBE and wB97XB and also the fully ab initio resolution of identity approximate coupled‐cluster method (gas‐phase only) are less accurate for all three complexes. The ground state (GS) two‐state approximation first hyperpolarisability β_2SA for 3 from RASPT2 is very close to that derived experimentally via hyper‐Rayleigh scattering, whereas the corresponding DFT‐based values are considerably larger. The β responses calculated by using B3LYP, B3P86 or M06 increase markedly as the π‐conjugation extends on moving along the series 2 → 4 , for both the GS and FDAES species. All three functionals predict substantial FDAES β enhancements for each complex, increasing with the π‐conjugation, up to about sevenfold for 4 . Also, the computed second hyperpolarisabilities γ generally increase in the FDAES, but the results vary between the different functionals.     

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (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 ω B97XD 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^?.     

Basis set convergence of indirect spin-spin coupling constants in the Kohn-Sham limit for several small molecules

The performance of more than 40 density functionals in predicting indirect spin-spin coupling constants (SSCCs) in the Kohn-Sham basis set limit was tested. For comparison, similar calculations were performed using the RHF, SOPPA, SOPPA(CC2), and SOPPA(CCSD) methods, and the results were estimated toward the complete basis set (CBS) limit. The SSCCs of nine small molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6), and C(6)H(6)) were calculated using the dedicated Jensen pcJ-n polarization-consistent basis sets and used for the CBS limit estimations within the Kohn-Sham limit. These CBS results were compared with calculations using the aug-cc-pVTZ-J basis set. Among the 41 studied DFT methods, the tHCTHhyb, HSEh1PBE, HSE2PBE, wB97XD, wB97, and wB97X functionals reproduced accurately the experimental (1)J(XH) SSCCs and (3)J(HH60) and (2)J(HH(gem)) in ethane. Similarly, the functionals HSEh1PBE, HSE2PBE, wB97XD, wB97, and wB97X predicted accurately (1)J(CC), and B98, B97-1, B97-2, PBE1PBE, B1LYP, and O3LYP provided accurate (1)J(CO) results in the CO molecule. A very good performance for the calculation of the SSCCs based on the use of the relatively small basis set aug-cc-pVTZ-J was observed.     

Hydrazones from hydroxy naphthaldehydes and N-aminoheterocycles: structure and stereodynamics

Schiff bases derived from 2-hydroxy-1-naphthaldehyde, or 1-hydroxy-2-naphthaldehyde, and different saturated N-aminoheterocycles have been prepared. Their structures have been elucidated in both solution and the solid state, including unequivocal X-ray diffraction analyses. Experimental data evidence the presence of imine (or hydrazone) structures as the most stable tautomers, while all attempts to switch to enamine (or enhydrazine) structures based on electronic and steric considerations were unsuccessful. A complete conformational analysis assisted by DFT calculations at B3LYP/6-31G^∗ and M06-2X/6-311++G^∗∗ levels has been performed on each series of representative structures.     

A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error

We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP.     

Quantum Chemical Study of Addition–Elimination Reactions of Dimethyl Carbonate with Methylamine

The mechanisms of noncatalytic and autocatalytic addition–elimination reactions of dimethyl carbonate with methylamine have been studied in terms of wB97XD/6-311++G(df,p), M06/6-311++G(df,p), and PBE0/6-311++G(df,p) quantum chemical methods, and thermodynamic and activation parameters of these reactions have been calculated. The rate-determining stage is the formation of tetrahedral carbon intermediate. The addition–elimination mechanism is preferred over the autocatalytic S_N2 mechanism determined by enhanced donor–acceptor and acid–base properties of amine complexes with alcohol associates in comparison to amines.     

The accuracy of DFT-optimized geometries of functional transition metal compounds: a validation study of catalysts for olefin metathesis and other reactions in the homogeneous phase

We have investigated the performance of eight popular density functionals, four of which are "standard" functionals not including dispersion (B3LYP, BP86, PBE, and TPSS) and four of which have been constructed to account for dispersion (B97D, wB97XD, M06, and M06L), in reproducing 18 molecular structures derived from single-crystal X-ray diffraction experiments on ruthenium-based olefin metathesis catalyst precursors. Our analysis of all the internuclear distances reveals that standard DFT predicts systematically expanded structures. In contrast, all the methods accounting for dispersion give rise to more compact structures, removing the systematic overestimation of internuclear distances. The contracting effect of dispersion is general and also affects chemical bonds, thus reducing the general overestimation of bond lengths. The best overall performance is observed for wB97XD, which offers relatively small statistical errors when considering the overall structure as well as selected distances. Only for the coordination center geometry is the accuracy of wB97XD matched by standard functionals such as PBE and TPSS, whereas M06 and M06L are associated with larger errors. At the other end of the scale, B3LYP is seen to give the largest statistical errors in general, both when considering the complete structures and the geometries of the coordination centers alone. For the organic ligands, however, B3LYP performs clearly better than the other standard functionals although not as well as the functionals accounting for dispersion. Extending the basis sets is seen to improve the structures in particular of the coordination center, thus underlining the importance of using sufficiently flexible basis sets if highly accurate geometries are to be obtained. Similar conclusions to those obtained for the ruthenium catalysts can be drawn from comparisons of the X-ray crystal structures of 10 other organometallic complexes of relevance to homogeneous catalysis, covering first (Ti, Fe, Co, Ni), second (Zr, Mo, Rh, Pd) and third (W, Ir) row transition metals, with those of DFT. The latter analyses thus offer a first indication that the picture obtained for the ruthenium alkylidene complexes may be extended to other classes of relatively large transition metal complexes.     

Computational studies on ethylene addition to nickel bis(dithiolene)

The density functionals B3LYP, B3PW91, BMK, HSE06, LC-ωPBE, M05, M06, O3LYP, TPSS, ω-B97X, and ω-B97XD are used to optimize key transition states and intermediates for ethylene addition to Ni(edt)(2) (edt = S(2)C(2)H(2)). The efficacy of the basis sets 6-31G**, 6-31++G**, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ is also examined. The geometric parameters optimized with different basis sets and density functionals are similar and agree well with experimental values. The ω-B97XD functional gives relative energies closest to those from CCSD, while M06 and HSE06 yield results close to those from CCSD(T). CASSCF and CASSCF-PT2 calculation results are also given. Variation of the relative energies from different density functionals appears to arise, in part, from the multireference character of this system, as confirmed by the T1 diagnostic and CASSCF calculations.     

Quantum chemical investigations on hydrogen bonding interactions established in the inclusion complex β-cyclodextrin/benzocaine through the DFT,AIM and NBO approaches

Structure and stability of an inclusion complex formed by Benzocaine (BZC) and β-cyclodextrin (β-CD) were investigated computationally using different levels of theory. The conformational research based on PM6 method allowed reach two minimum-energy structures: model A and model B. The lowest conformers have been exposed to fully geometry optimization employing four DFT functionals: B3LYP, CAM-B3LYP, M05-2X and M06-2X. The performed DFT calculations have identified the model B, in which the amino group is located at the primary face of β-CD, as the most stable complex by an amount up to ?40 kcal/mol. Further, the greater stabilization of model B in respect to model A, has been ascertained through AIM and NBO analyses which clarified the main hydrogen bonds HBs interactions governing the reactivity of BZC inside the hydrophobic cavity of β-CD. Finally, the estimated isotropic ¹H nuclear magnetic shielding constants generated from the gauge-including-atomic-orbital calculation have been analyzed and then compared with the available experimental data.     

Assessment of ab initio MP2 and density functionals for characterizing the potential energy profiles of the SN2 reactions at N center

The potential energy profiles of five selected bimolecular nucleophilic substitution (S_N2) reactions at nitrogen (N) center have been reinvestigated with the CCSD(T), G3[MP2,CCSD(T)], MP2, and some density functional methods. The basis sets of 6‐31+G(d,p) and 6‐311+G(3d,2p) are used for the MP2 and density functional calculations. Taking the relative energies at the CCSD(T)/CBS level of theory as benchmarks, we recommend the MP2, B97‐K, B2K‐PLYP, BMK, ωB97X‐D, M06‐2X, M05‐2X, CAM‐B3LYP, M08‐SO, and ωB97X methods to generally characterize the potential energy profiles for the S_N2 reactions at N center. Furthermore, these recommended methods with the relatively small 6‐31+G(d,p) basis set may also be used to perform direct classical trajectory simulations to uncover the dynamic behaviors of the S_N2 reactions at N center. © 2012 Wiley Periodicals, Inc.     

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

In recent years, there has been an increased interest in understanding the enzymatic mechanism of glycosidases resorting mostly to DFT and DFT/MM calculations. However, the performance of density functionals (DFs) is well known to be system and property dependent. Trends drawn from general studies, despite important to evaluate the quality of the DFs and to pave the way for the development of new DFs, may be misleading when applied to a single specific system/property. To overcome this issue, we carried out a benchmarking study of 40 DFs applied to the geometry optimization and to the electronic barrier height (E _Barrier) and electronic energy of reaction (E _R) of prototypical glycosidase‐catalyzed reactions. Additionally, we report calculations with SCC‐DFTB and four semiempirical MO methods applied to the same problem. We have used a universal molecular model for retaining glycosidases, comprising only a 22‐atoms system that mimics the active site and substrate. High accuracy reference geometries and energies were calculated at the CCSD(T)/CBS//MP2/aug‐cc‐pVTZ level of theory. Most DFs reproduce the reference geometries extremely well, with mean unsigned errors (MUE) smaller than 0.05 Å for bond lengths and 3° for bond angles. Among the DFs, wB97X‐D, CAM‐B3LYP, B3P86, and PBE1PBE have the best performance in geometry optimizations (MUE = 0.02 Å). Conversely, semiempirical MO and SCC‐DFTB methods yielded less accurate geometries (MUE between 0.09 and 0.17 Å). The inclusion of D3 correction has a small, but still relevant, influence in the geometry predicted by some DFs. Regarding E _Barrier, 11 DFs (MPW1B95, CAM‐B3LYP, M06 ‐ 2X, PBE1PBE, wB97X ‐ D, B1B95, BMK, MN12 – SX, M05, M06, and M11) presented errors below 1 kcal.mol^?1, in relation to the reference energy. Most of these functionals belong to the family of hybrid functionals (H‐GGA, HH‐GGA, and HM‐GGA), which shows a positive influence of HF exchange in the determination of E _Barrier. The inclusion of D3 correction has not affected significantly the E _Barrier and E _R. The use of geometries at the accurate but expensive MP2/aug‐cc‐pVTZ level of theory has a small, albeit not insignificant, influence in the E _Barrier when compared with energies calculated with geometries determined with the DFs (usually a few tenths of kcal.mol^?1, with exceptions). In general, semiempirical MO methods and DFTB are associated with larger errors in the determination of E _Barrier, with unsigned errors from 6.9 to 24.7 kcal.mol^?1.     

Conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete

The conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory, and density functional theory and employing the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single-point fourth-order perturbation theory, CCSD, and CCSD(T) calculations employing the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectfully, to ascertain the contribution of higher order correlation. Three DFT functionals, B3LYP, wB97XD, and M06-2X, are employed to determine whether they can yield results similar to those obtained at the CCSD(T) level.     

DFT studies of ESR parameters for N?O centered radicals,N‐alkoxyaminyl and aminoxyl radicals

Theoretical calculations of ESR parameters for aminoxyl radicals have been widely studied using the density functional theory (DFT) calculations. However, the isomer N‐alkoxyaminyl radicals have been limitedly studied. With the use of experimental data for 46 N‐alkoxyaminyl and 38 aminoxyl radicals, the isotropic ¹⁴N hyperfine coupling constants (a_N) and g‐factors have been theoretically estimated by several DFT calculations. The best calculation scheme of a_N for N‐alkoxyaminyl radicals was PCM/B3LYP/6‐31 + + G(d,p) (R² = 0.9519, MAE = 0.034 mT), and that for aminoxyl radicals was PCM/BHandHLYP/6‐31 + + G(3df,3pd) (R² = 0.9336, MAE = 0.057 mT). For aminoxyl radicals, the solvation models in calculations enhanced the accuracy of reproducibility. In contrast, for N‐alkoxyaminyl radicals the calculations with solvation models provided no improvement. The differences in the best functionals between two types of radicals were thought to come from the contribution ratios of neutral and dipolar canonical structures in resonance forms. The a_N for N‐alkoxyaminyl radicals that were stabilized by small contribution of dipolar canonical structures could be precisely reproduced by B3LYP with only 20% HF exact exchange. In contrast, the a_N for aminoxyl radicals stabilized by large contribution of dipolar canonical structures was well reproduced by BHandHLYP with 50% HF exchange. The best calculation scheme of g‐factors was IEFPCM/B3LYP/6‐31 + G(d,p) (R² = 0.9767, MAE = 0.0001) for not only aminoxyl but also N‐alkoxyaminyl radicals. Copyright © 2011 John Wiley & Sons, Ltd.     

Base pairing patterns of DNA base lesion spiroiminodihydantoin: A DFT study

The DNA base lesion spiroiminodihydantoin (Sp) is produced in biological systems endogenously and can cause mutation and cancer. It is considered to be more mutagenic and deleterious than 8‐oxoguanine and other oxidized guanine products such as guanidinohydantoin (Gh) and imidazolone. In this work, the base pairing patterns of Sp with each of the normal nucleic acid bases of DNA have been investigated thoroughly using the B3LYP, M06‐2X, and wB97X‐D functionals of density functional theory in conjunction with the aug‐cc‐pVDZ basis set. It is found that the magnitudes of interaction energies between the bases and Sp follow the order: Sp‐guanine >> Sp‐cytosine > Sp‐adenine > Sp‐thymine. The strong Sp‐guanine abnormal base pairing may be the main cause of the observed mutagenicity of Sp. © 2013 Wiley Periodicals, Inc.     

Vibrational spectra and reinvestigation of the crystal structure of a polymeric copper(II)-orotate complex, [Cu(μ-HOr)(H2O)2]n: The performance of new DFT methods, M06 and M05-2X, in theoretical studies

The crystal and molecular structure of a polymeric Cu(II)-orotate complex, [Cu(μ-HOr)(H₂O)₂]_n, has been reinvestigated by single crystal X-ray diffraction. It is shown that several synergistic interactions: two axial Cu-O interactions; intramolecular and intermolecular hydrogen bonds; and π-π stacking between the uracil rings contribute to the stability of the crystal structure. The Raman and FT-IR spectra of the title complex are reported for the first time. Comprehensive theoretical studies have been performed by using three unrestricted DFT methods: B3LYP; and the recently developed M06, and M05-2X density functionals. Clear-cut assignments of all the bands in the vibrational spectra have been made on the basis of the calculated potential energy distribution, PED. The very strong Raman band at 1219 cm⁻¹ is diagnostic for the N1-deprotonation of the uracil ring and formation of the copper-nitrogen bond, in this complex. The Cu-O (carboxylate) stretching vibration is observed at 287 cm⁻¹ in the IR spectrum, while the Cu-N (U ring) stretching vibration is assigned to the strong Raman band at 263 cm⁻¹. The molecular structure and vibrational spectra (frequencies and intensities) calculated by the M06 functional method are very similar to the results obtained by the B3LYP method, but M06 performs better than B3LYP in calculations of the geometrical parameters and vibrational frequencies of the interligand O-H?O hydrogen bonding. Unfortunately, the M05-2X method seriously overestimates the strength of interligand hydrogen bond.     

Computational Study of Cage Like (ZnO)12 Cluster Using Hybrid and Hybrid Meta Functionals

Density Functional Theory employing hybrid and M06 functionals in combination with three different basis sets is used to calculate the ground state of a cage like (ZnO)₁₂ nanocluster which has been consistently reported as the more stable cluster for its particular size. B3LYP and B3PW91 hybrid functionals combined with 6‐31+G*, Lanl2dz and SDD basis sets are employed to treat the ZnO molecular system. Alternatively, three M06 functionals in combination with three basis sets are employed in the nanostructure calculations. Results obtained by treating ZnO sodalite cage nanocluster with M06 functionals demonstrated comparable quality to results obtained with hybrid functionals. Within this study, efficient theoretical DFT methods with the widely known hybrid and the recently created M06 meta‐hybrid functionals are employed to study nanostructured ZnO. Our resulting parameters provide a fresh approach performance wise on the different theoretical methods to treat transition metal nanostructures, particularly, ZnO nanoclusters geometry and electronic structure.