Hybrid Density Functional Method Research Articles

DFT, FT-Raman, FT-IR, liquid and solid state NMR studies of 2,6-dimethoxyphenylboronic acid

Possible stable forms and molecular structures of 2,6-dimethoxyphenylboronic acid (2,6-dmpba) were studied experimentally and theoretically using FT-IR, Raman, liquid–solid state NMR and XRD spectroscopic methods. FT-IR and Raman spectra were recorded in the region of 4000–200 cm −1. 13C cross-polarization magic-angle spinning NMR and liquid phase 1H, 13C and HETCOR NMR spectra of 2,6-dmpba ((CH 3O) 2C 6H 3B(OH) 2) were reported. The optimized geometric structures concerning to the minimum on the potential energy surface was investigated by Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method together with 6-31++G(d,p) basis set. Vibrational wavenumbers and 1H, 13C NMR chemical shifts of 2,6-dmpba were calculated by means of B3LYP density functional methods with 6-31++G(d,p) basis set. Comparison between the experimental and theoretical results indicates that density functional B3LYP method is able to provide satisfactory results for predicting vibrational wavenumbers and nuclear magnetic shielding tensors. Furthermore, reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method.

A theoretical study of the carbenoids LiCH2X (X = Cl, Br, I) cyclopropanation reaction with ketene

A computational study for the [2 + 1] addition of the lithium carbenoids LiCH2X (X = Cl, Br, I) with ketene have been investigated by means of the B3LYP hybrid density functional method. All the reactions examined displayed similar concerted mechanisms for the cyclopropanation of these reagents. The lithium carbenoids react with ketene via an asynchronous attack on one CH2 or C group of ketene with relatively low barrier to reaction in the range of 25·34–33·74 kJ/mol in THF solvent. The trend of the lithium carbenoids reaction barrier with ketene is LiCH2Cl < LiCH2Br < LiCH2I. The results show that the reactions could be highly chemical reactivity with low barriers and could be favoured in experiment. The reactions could proceed easily at lower temperature. The computational results are briefly compared to other carbenoid reactions and related species.

Effect of CH 3CO functional group on the molecular and electronic properties of BN43zz nanotube: A computational chemistry study

The geometric and electronic structures of the CH 3CO functionalized BN43 zigzag nanotube (BN43zz NT) were studied by means of the B3LYP hybrid density functional method using 6-31G(d) basis set. The position of CH 3CO molecule on top of tube plays an important role on the tube–CH 3CO interaction. Two types functionalized BN43zz NTs were found in interaction between CH 3CO and BN43zz NT. It is energetically favorable for the CH 3CO radical to interact with the slanted B–N bonds (in S type complexes with stronger adsorption energy) which are perpendicular to the tube axis. The more stable functionalized BN43zz NTs prefer open structure rather than closed four-membered-ring one. The HOMO–LUMO gap, electronic chemical potential μ, hardness η, softness S and electrophilicity index ω for CH 3CO, BNNT and different configurations of functionalized BNNT in gas and polar solvent phases were calculated. These results show that the functionalization of BN43zz NT results in significant changes in the electronic properties of BNNTs. It is predicted that the conductivity of the nanotube increases upon adsorption of the CH 3CO molecule on the tube. To gain a deep understanding of the electron delocalization in complexes, nucleus-independent chemical shift (NICS) analysis have been performed at B3LYP/6-31G(d) level using GIAO method. The results obtained by natural bond orbital (NBO) analysis showed that in the S and P complexes charge transfer occurs from BNNT to CH 3CO and vice versa, respectively. Theory of atoms in molecules (AIM) was also applied to characterize B–O and N–C bonds in nanotubes.

Vibrational spectroscopic investigation and conformational analysis of 1-cyclohexylpiperazine

The possible stable conformers of 1-cyclohexylpiperazine (1-chpp) molecule were experimentally and theoretically studied by FT-IR and Raman spectroscopy in the region of 4000–200 cm −1. The optimized geometric structures concerning to the minimum on the potential energy surface were investigated by B3LYP hybrid density functional theory method together with 6-31G(d) basis set. Comparison between the experimental and theoretical results indicates that density functional B3LYP method is able to provide satisfactory results for predicting vibrational wavenumbers and equatorial–equatorial (e–e) form is supposed to be the most stable form of 1-chpp molecule.

Theoretical investigation on the presence of different iron sites in RbMn[Fe(CN)6]·H2O

The 57Fe electron contact densities and the corresponding Mössbauer isomer shifts of RbMn[Fe(CN)6]·H2O are calculated with the use of ab initio wavefunction methods and double hybrid density functional method. The theoretical analysis of possible origin of the two slightly different signals in the Mössbauer spectra observed at 293 K and 50 K (Vertelman et al. 2008 Chem. Mater. 20 1236-38) is carried out. The measured differences of 0.083 – 0.105 mm/s between the high-temperature and low-temperature phases can be attributed to the different oxidation states of iron: the iron is in FeIII oxidation state in the high temperature phase and FeII state in the low temperature phase. The smaller isomer shift differences of 0.012 – 0.034 mm/s occurring in both high temperature and low temperature structures can be attributed to different distributions of the RbI ions within the unit cell of RbMn[Fe(CN)6]·H2O.

Structures and energies of the radicals and anions generated from chlorpyrifos

The radicals and anions generated from chlorpyrifos by removing a hydrogen atom have been investigated using the hybrid density functional B3PW91 method. The results show that all the radicals have been classified as three groups and their stability order is methylene (radical 1, 3, 5, and 7) > methyl (radical 9, 11 and 13) > ring (15); the anions have the relative energetic order: methyl > methylene > ring. Moreover, some decomposition reactions are also reported. The large HOMO-LUMO gaps indicate that both radicals and anions are predicted to be high-kinetic stable molecules. We also find that radicals 9, 11 and 13 have the highest AEAs and anions 2, 4 and 6 have higher VDEs. Additionally, natural population analysis charges show that there is the lowest Deltaq (0.14) for the C7 and C9 atoms. We hope that our theoretical results may provide a reference for further experiment and practical application.

THEORETICAL STUDY ON METHANE HYDROXYLATION BY MIMIC METHANE MONOOXYGENASE WITH bis(μ-OXO)DIMANGANESE CORE

The reaction mechanism for methane hydroxylation catalyzed by mimic methane monooxygenase (MMO) with bis(μ-oxo)dimanganese core has been investigated on the septet and nonet potential energy surfaces by hybrid density functional method B3LYP. The key reactive compound Q of MMO was modeled by trans- (H2CNH)(COOH) Mn(μ-O)2(μ-HCOO)2Mn(H2CNH)(COOH) . The ground state of Q is located on the septet state, which has a diamond-core structure with two Mn(IV) atoms. It is shown that the reaction proceeds via a radical-rebound mechanism, in which the step of C–H cleavage is the rate-determining step both in the gas phase and solution. Furthermore, the reaction may proceed more easily as the polarity of solution is larger. On the other hand, the kinetic isotope effects (KIEs) for H atom abstraction from methane are taken into account on the basis of transition state theory with Wigner tunneling corrections. The mimic MMO with bis(μ-oxo)dimanganese core might be an effective mimic catalyst for methane hydroxylation.

КВАНТОВОХИМИЧЕСКОЕ ИССЛЕДОВАНИЕ И QSAR-СВОЙСТВА АРОМАТИЧЕСКИХ ПРОИЗВОДНЫХ З-СЕЛЕНПЕНТАН-ДИОНА-1,5: ПРЕДПОСЫЛКИ ВЗАИМОДЕЙСТВИЯ С УГЛЕВОДСВЯЗЫВАЮЩИМИ БЕЛКАМИ

The role of spatial and electronic structure, hydrophobic properties and concentration of organoselenium compounds on their interaction with fungal metabolites - carbohydrate-binding proteins, extracellular lectins of Lentinula edodes (shiitake mushroom) has been consi­ dered. By the hybrid density functional theory method at the B3LYP/6-31G(d,p) theory level, spatial and electronic structure of the 1,5-di(4-R-phenyl)-3-selenopentanediones-1,5 molecules has been studied. By means of the QSAR properties evaluation by the atomic- bonding-additive schemes, the distinct hydrophobicity of these com­ pounds has been demonstrated. The theoretical characteristics thus obtained have been used for interpreting the experimental data on the lectin activity enhancement in the presence of 1,5-di(4-R-phenyi)- 3-selenopentanediones-1,5, as well as on the greatest efficiency of ethoxy derivative.

Theoretical study of electronic structures of [(H2O)3(O-)Mn(μ-oxo)2Mn(OH2)4]q+ (q = 2 or 3) with Mn–O bond

Molecular geometries and electronic structures of manganese binuclear complexes, [(H(2)O)(3)(O-)Mn(bis-mu-oxo-O(2))Mn(OH(2))(4)](q+) (q = 2 or 3), which are model complexes of the S(3) state in the Kok cycle of OEC, were examined using hybrid density functional theory and broken symmetry method. The complexes of q = 2 and 3, which have a Mn-O bond, correspond to those derived from Mn(2)(II,III) and Mn(2)(III,III) at the S(0) state of the Kok cycle. The conformers with the Mn-O bond axial to the Mn(2)O(2) core are lower in energy than those with the equatorial Mn-O bond. The equatorial Mn-O bonds are assigned as Mn(III)-O*(-) and Mn(IV)-O*(-) for M(2)(II,III) and M(2)(III,III) series, respectively. The axial Mn-O bonds are Mn(IV)=O(2-) for M(2)(II,III) and Mn(IV)-O*(-) for Mn(2)(III,III). The characters of Mn-O orbitals are pi-orbitals composed of d-p interactions. The conformer with the axial Mn(IV)=O(2-) derived from M(2)(II,III) at S(0) is thermochemically unstable, leading to proton transfer to give two OHs in the complex, while the axial Mn(IV)-O*(-) from Mn(2)(III,III) at S(0) is stable without the proton transfer. The magnetic interactions between two Mn ions and O were also examined by estimations of effective exchange integrals.

Vibrational spectroscopic and conformational studies of 1-(4-pyridyl)piperazine

AbstractPossible stable conformers of the 1-(4-pyridyl)piperazine (1-4pypp) molecule were experimentally and theoretically studied by FT-IR and Raman spectroscopy. FT-IR and Raman spectra were recorded in the region of 4000–200 cm−1. Optimized geometric structures related to the minimum on the potential energy surface were investigated by the B3LYP hybrid density functional theory method using the 6-31G(d) basis set. Comparison of the experimental and theoretical results indicates that the density functional B3LYP method provides satisfactory results for the prediction of vibrational wavenumbers and structural parameters and equatorial-equatorial (e-e) isomer is supposed to be the most stable form of the 1–4pypp molecule.

REEXAMINATION OF LOW ENERGY STRUCTURES OF ${\rm Au}_{4}^{-}$ AND Au4

Low energy isomers of [Formula: see text] and Au4 were reexamined using the hybrid density functional B3LYP method and the couple-cluster method with the aug-cc-pVDZ-PP and aug-cc-pVTZ-PP basis sets. For [Formula: see text], the B3LYP method favors the zigzag isomer and the second order Moller–Plesset perturbation (MP2) total energy calculation favors the D2h rhombus isomer, whereas the couple-cluster singles and doubles with perturbative triples [CCSD(T)] level of theory favors the Y-shaped C2v isomer. The pyramid isomer is much higher in energy and could be easily excluded. The Gibbs free energy correction based on harmonic approximation suggests that the zigzag isomer is lower in free energy than the D2h rhombus isomer at 298.15 K. These results confirm that the Y-shaped C2v isomer is the global minimum at both 0 K and room temperature and is thus the major isomer to account for the experimental photoelectron spectrum. The zigzag isomer is suggested, as a minor isomer, to account for the weak second peak at 3.40 eV in the experimental photoelectron spectrum. For neutral Au4 , the zigzag isomer is more stable than D2h rhombus isomer at the B3LYP level and the D2h rhombus isomer is the global minimum on basis of all post Hartree–Fock levels of theory.

DFT studies of the degradation mechanism of methyl mercury activated by a sulfur-rich ligand

We describe theoretical insights into the mechanism of Hg-C bond protonolysis in methyl mercury coordinated by the tris(2-mercapto-1-tert-butylimidazolyl)hydroborato ligand, the structural and functional analogue of the organomercurial lyase MerB. Different cleavage pathways including both frontside and backside attack transition states were systematically studied by the hybrid density functional method B3LYP. Dependence of Hg-C bond activation on the primary sulfur coordination number of mercury was elaborated, and conceptual DFT indexes were suggested to be more appropriate than gross charge of atom sites in interpreting the dependence. Furthermore, absence of configurational inversion in MerB-catalyzed reactions was accounted for by examinations of the backside protonolysis pathways in the present system. Lastly, a rationalization was provided about the choice between different characteristics of transition states including both four-center and six-center ones.

DFT B3LYP calculation of the spatial structure of Co(II), Ni(II), and Cu(II) template complexes formed in ternary systems metal(II) ion-dithiooxamide-formaldehyde

The hybrid density functional theory B3LYP method with the 6-31G(d) basis set and the Gaussian 98 program has been used for calculating the geometric parameters of the Mn(II), Co(II), Ni(II), and Cu(II) complexes with NNSS-donor macrocyclic ligands forming in the course of template processes in the M(II)-dithiooxamide-formaldehyde systems. The bond lengths and bond angles in the complexes with the MN2S2 metal chelate core are reported. For all M(II) ions, the extra six-membered chelate ring that form as a result of template assembly is rotated through a rather large angle with respect to two five-membered rings and the ring itself is not planar.

Conformational preferences and prolyl cis–trans isomerization of phosphorylated Ser/Thr‐Pro motifs

The conformational study on Ac-pSer-Pro-NHMe and Ac-pThr-Pro-NHMe peptides has been carried out using hybrid density functional methods with the implicit solvation reaction field theory at the B3LYP/ 6-311++G(d,p)//B3LYP/6-31+G(d) level of theory in the gas phase and in solution (chloroform and water). For both pSer-Pro and pThr-Pro peptides in the gas phase and in chloroform, the most preferred conformation has the alpha-helical structure for the pSer/pThr residue, the down-puckered polyproline I structure for the Pro residue, and the cis prolyl peptide bond between the two residues, in which two hydrogen bonds between the phosphate oxygens with the backbone N--H groups seem to play a role. However, the trans conformations that have a single hydrogen bond of the phosphate oxygen with either of two backbone N--H groups become most preferred for both peptides in water. This is because the hydration free energy of the anionic oxygen of the phosphate group is expected to dramatically decrease for the cis conformation upon formation of the hydrogen bond with the backbone N--H groups. These calculated results are consistent with the observations by NMR and IR experiments, suggesting the existence of hydrogen bonds between the charged phosphoryl group and the backbone amide protons in solution. The calculated cis populations of 14.7 and 14.2% and rotational barriers of 19.87 and 20.57 kcal/mol to the cis-to-trans isomerization for pSer-Pro and pThr-Pro peptides in water, respectively, are consistent with the observed values for pSer-Pro and pThr-Pro containing peptides from NMR experiments. However, the hydrogen bond between the prolyl nitrogen and the following amide N--H group, which was suggested to be capable of catalyzing the prolyl isomerization, does not play a role in stabilizing the preferred transition state for the pSer/pThr-Pro peptides in water. Instead, the amide hydrogen of the NHMe group is involved in a bifurcated hydrogen bond with the anionic oxygen and phosphoester oxygen of the phosphate group.

A Reliable Quantum-Chemical Protocol for the Characterization of Organic Mixed-Valence Compounds

Structures, dipole moments, electron-transfer barriers, and spin density distributions of a series of mixed-valent bistriarylamin radical cations have been studied systematically by hybrid density functional methods with variable exact-exchange admixture combined with a continuum solvent model. The chosen systems differ in their bridging units and are all relatively close, from both sides, to the class II/III borderline of the Robin-Day classification of mixed-valence systems. Solvent effects are found to have a dramatic influence on the localized vs delocalized character of these cations. While gas-phase calculations or computations in a nonpolar solvent place all systems on the delocalized class III side, a more polar solvent like acetonitrile enables observation of symmetry breaking and charge localization with moderate exact-exchange admixtures in a hybrid functional for the systems on the class II side (with diphenylbutadiyne and diphenylethyne bridges). In contrast, the cations with the shortest bridges (phenylene, biphenylene) are characterized as class III. The comparison of computed intervalence charge-transfer excitation frequencies with experiment confirms the system with the diphenylbutadiyne bridge, and probably the system with the diphenylethyne bridge, to be class II, whereas in the dichloromethane solvent employed for spectroscopic measurements, the two other systems are on the class III side. Nonstandard hybrid density functional calculations with 35% Hartree-Fock-like exchange combined with continuum solvent models are suggested as a practical protocol for the quantum-chemical characterization of organic mixed-valence systems. This approach should allow closer examinations and provides a basis for the evaluation of other computational methods.

Effects of Restricted Rotations and Dynamic Averaging on the Calculated Isotropic Hyperfine Coupling Constants of the bis-Dimethyl and bis-Di(trifluoromethyl) Nitroxide Radicals

The rotational effects of the CH(3) and CF(3) groups on the electronic structure and nuclear hyperfine coupling constants (HFCCs) in dimethylnitroxide (DMNO*) and ditrifluoro-methynitroxide (TFMNO*) are investigated using the UB1LYP hybrid density functional method. The CH(3) and CF(3) HFCCs of both radicals are found to obey the McConnell relation during rotation. The two CH(3) groups of the DMNO* do not gear with each other, but the rotation of the first CH(3) group induces only a small rocking effect ( approximately 7 degrees ) in the second group. However, in TFMNO*, the fluorine atoms from different CF(3) groups are close enough so that the steric repulsion between them causes them to act as two interlocked gears, where one drives the other. Therefore, both CF(3) groups undergo full rotation. To the best of our knowledge, this is only the second example of "gearing" to be studied. Stabilization due to hyperconjugation is also a major factor that affects the magnitudes of the HFCCs of the CF(3) groups during rotational averaging. Stable configurations at specific CF(3) group orientations have a large overlap with the NO pi-electron cloud because the lobes of the hybridized p(sigma)(F(2)), p(sigma)(F(3)), p(sigma)(F(5)), and p(sigma)(F(6)) orbitals along the F-C bonds have cylindrical symmetry and are of the correct phases for hyperconjugation to occur. The calculated TFMNO* C(1)-N and C(2)-N bond orders range from 0.91 to 0.95 as the CF(3) groups are rotated. Therefore, the C-N bonds are essentially single bonds. This, in conjunction with the low rotational energy barrier of approximately 50 cm(-1), explains why the EPR intensities of the (19)F hyperfine splittings, in the range of 163-297 K, are characteristic of six equivalent rapidly rotating fluorine atoms. The TFMNO* out-of-plane NO vibrations induce additional s character at the (14)N nucleus. This increases the magnitude of the (14)N HFCC and decreases the (19)F HFCCs. As the temperature increases and because of mixing of the first excited out-of-plane vibrational state, the NO vibrational amplitudes also increase. This leads to an increased (14)N HFCC and decreased (19)F HFCCs, which is in agreement with experiment.

A DFT study of carbon monoxide adsorption on a Si4 nano-cluster

Using the gradient-corrected hybrid density functional method of Predew, Burke, and Ernzerhof (PBEPBE) and the new hybrid meta-density functional method of Truhlar (MPW1B95), the geometry, adsorption energy, vibrational frequency, and charge distribution of carbon monoxide adsorption on a Si4 nano-cluster has been studied. Taking into account spin multicipility in the calculations, a new stable structure of CO absorbed on the Si4 cluster has been found, in addition to the previously reported structures. Exhaustive vibrational frequency analysis of optimized structures shows that some of the formerly reported structures have imaginary vibrational frequencies and are not proper stable structures. Thus, they do not represent real local energy minima. Also, CO vibrational frequency analysis shows that a significant change of vibrational frequency in the stable structures occurs.

The reaction mechanism of phenylethanolamine N-methyltransferase: A density functional theory study

Hybrid density functional theory methods were used to investigate the reaction mechanism of human phenylethanolamine N-methyltransferase (hPNMT). This enzyme catalyzes the S-adenosyl- l-methionine-dependent conversion of norepinephrine to epinephrine, which constitutes the terminal step in the catecholamine biosynthesis. Several models of the active site were constructed based on the X-ray structure. Geometries of the stationary points along the reaction path were optimized and the reaction barrier and energy were calculated and compared to the experimental values. The calculations demonstrate that the reaction takes place via an S N2 mechanism with methyl transfer being rate-limiting, a suggestion supported by mutagenesis studies. Optimal agreement with experimental data is reached using a model in which both active site glutamates are protonated. Overall, the mechanism of hPNMT is more similar to those of catechol O-methyltransferase and glycine N-methyltransferase than to that of guanidinoacetate N-methyltransferase in which methyl transfer is coupled to proton transfer.

Assessment of the "6-31+G** + LANL2DZ" mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionization potentials for first-row-transition-metal complexes.

Computational chemists have long demonstrated great interest in finding ways to reliably and accurately predict the molecular properties for transition-metal-containing complexes. This study is a continuation of our validation efforts of density functional theory (DFT) methods when applied to transition-metal-containing systems (Riley, K.E.; Merz, K. M., Jr. J. Phys. Chem. 2007, 111, 6044-6053). In our previous work we examined DFT using all-electron basis sets, but approaches incorporating effective core potentials (ECPs) are effective in reducing computational expense. With this in mind, our efforts were expanded to include evaluation of the performance of the basis set derived to approximate such an approach as well on the same set of density functionals. Indeed, employing an ECP basis such as LANL2DZ (Los Alamos National Laboratory 2 double zeta) for transition metals, while using all-electron basis sets for all other non-transition-metal atoms, has become more and more popular in computations on transition-metal-containing systems. In this study, we assess the performance of 12 different DFT functionals, from the GGA (generalized gradient approximation), hybrid-GGA, meta-GGA, and hybrid-meta-GGA classes, respectively, along with the 6-31+G** + LANL2DZ (on the transition metal) mixed basis set in predicting two important molecular properties, heats of formation and ionization potentials, for 94 and 58 systems containing first-row transition metals from Ti to Zn, which are all in the third row of the periodic table. An interesting note is that the inclusion of the exact exchange term in density functional methods generally increases the accuracy of ionization potential prediction for the hybrid-GGA methods but decreases the reliability of determining the heats of formation for transition-metal-containing complexes for all hybrid density functional methods. The hybrid-GGA functional B3LYP gives the best performance in predicting the ionization potentials, while the meta-GGA functional TPSSTPSS provides the most reliable and accurate results for heat of formation calculations. TPSSTPSS, a meta-GGA functional, which was constructed from first principles and subject to known exact constraints just like in an "ab initio" way, is successful in predicting both the ionization potentials and the heats of formation for transition-metal-containing systems.

Theoretical study on third-order nonlinear optical properties in hexagonal graphene nanoflakes: Edge shape effect

Using hybrid density functional theory methods, we investigate the second hyperpolarizabilities ( γ) of hexagonal shaped finite graphene fragments, which are referred to as hexagonal graphene nanoflakes (HGNFs), with two types of edge shapes: zigzag (Z) and armchair (A) edges. It is found that Z-HGNF, which gives intermediate diradical characters ( y), exhibits about 3.3 times larger orthogonal components of γ ( γ xxxx = γ yyyy in this case) than A-HGNF, which gives zero y value (closed-shell system). The γ density analysis reveals that this enhancement originates in the significant contribution of γ densities on edge regions in Z-HGNF. These observations strongly indicate that Z-HGNF is a promising candidate of open-shell singlet NLO systems.