Theoretical study of the adsorption of pentachlorophenol on the pristine and Fe-doped boron nitride nanotubes.

To explore the novel application of boron nitride nanotubes (BNNTs), we investigated the interaction of pentachlorophenol (PCP) pollutant with the pristine and Fe doped (Fe-doped) (8, 0) single-walled BNNTs by performing density functional theory calculations. Compared with the weak physisorption on the pristine BNNT, PCP molecule presents strong chemisorption on the Fe-doped BNNT. The calculated data for the electronic properties indicate that doping Fe atom into the BNNT significantly improves the electronic transport property of BNNT, induces magnetism in the BNNT, and increases its adsorption sensitivity toward PCP molecule.

Molecular dynamics simulation of pyrene solubilized in a sodium dodecyl sulfate micelle.

In the present work, the structural and dynamical aspects of the solubilization process of pyrene within a sodium dodecyl sulfate micelle were studied using molecular dynamics simulations. Our results showed that free pyrene as the fluorescence probe can be spontaneously solubilized into the micelle and prefers to be located in the hydrophobic core region. As the local concentration of pyrene increased, two molecular probes could enter into the core hydrophobic region and the excited dimer of pyrene molecules was formed, showing a stacking mode of π-π conjugation.

Theoretical investigation on the chiral diamine-catalyzed epoxidation of cyclic enones: mechanism and effects of cocatalyst.

The asymmetric epoxidation of 2-cyclohexen-1-one with aqueous H(2)O(2) as oxidant, 1,2-diaminocyclohexane as catalyst, and a Brønsted acid trifluoroacetic acid (TFA) as cocatalyst has been studied by performing density functional theory calculations. It is confirmed that the catalyzed epoxidation proceeds via sequential nucleophilic addition and ring-closure processes involving a ketiminium intermediate. Four possible pathways associated with two Z isomers and two E isomers of ketiminium have been explored in detail.

Microscopic wetting of self-assembled monolayers with different surfaces: a combined molecular dynamics and quantum mechanics study.

Molecular dynamics simulations are used to study the micronature of the organization of water molecules on the flat surface of well-ordered self-assembled monolayers (SAMs) of 18-carbon alkanethiolate chains bound to a silicon (111) substrate. Six different headgroups (-CH(3), -C═C, -OCH(3), -CN, -NH(2), -COOH) are used to tune the character of the surface from hydrophobic to hydrophilic, while the level of hydration is consistent on all six SAM surfaces. Quantum mechanics calculations are employed to optimize each alkyl chain of the different SAMs with one water molecule and to investigate changes in the configuration of each headgroup under hydration.

Molecular dynamics study of the effect of calcium ions on the monolayer of SDC and SDSn surfactants at the vapor/liquid interface.

The effect of Ca(2+) ions on the hydration shell of sodium dodecyl carboxylate (SDC) and sodium dodecyl sulfonate (SDSn) monolayer at vapor/liquid interfaces was studied using molecular dynamics simulations. For each surfactant, two different surface concentrations were used to perform the simulations, and the aggregation morphologies and structural details have been reported. The results showed that the aggregation structures relate to both the surface coverage and the calcium ions.

Insights into the control of magnetic coupling in the Mn4(III) complex: from ferromagnetic to antiferromagnetic.

Magnetic coupling interactions of a Mn(III)(4) system are investigated by calculations based on density functional theory combined with a broken-symmetry approach (DFT-BS). Three different interactions including ferromagnetic and antiferromagnetic coupling are concomitant in this complex. This magnetic phenomenon of the complex is due to the different bridging angles between the Mn(III) centers in the three different models and the orbital complementarity of the μ-pzbg and μ-OCH(3) bridging ligands, which is proven by the analyses of the molecular orbitals.

First-principle conformational analysis of glycine residues in the alphabeta-tubulin dimer.

Amino acids, especially glycine, have been extensively studied whereas their conformational behaviors in proteins are rather limited. In this work, all the polypeptides containing glycine residues are truncated from the alphabeta-tubulin dimer and refined with the partial optimization technique, where the backbone atoms of the previous and posterior residues to the glycine residues are fixed at the experimental Cartesian positions whereas the others fully relaxed. The combination of the polypeptide models and partial optimization technique is validated by twolayer ONIOM calculations, being effective to retain the local structures of proteins and meanwhile optimizing the concerned glycine residues towards energy minima.

Effect of Ca2+ and Mg2+ ions on surfactant solutions investigated by molecular dynamics simulation.

The effect of Ca(2+) and Mg(2+) on the H-bonding structure around the headgroup of the surfactants sodium dodecyl sulfate (SDS) and sodium dodecyl sulfonate (SDSn) in solution has been studied by molecular dynamics simulation. Our results show that binding between the headgroup of the surfactant and Ca(2+) or Mg(2+) is prevented by a stabilizing solvent-separated minimum formed in the potential of mean force (PMF) between the interacting ion-pair. Among the contributions to the PMF, the major repulsive interaction is due to the rearrangement of the hydration shell after the ions enter into the original H-bonding structure of water around the headgroup, leading to a decrease in the number of H-bonds and an increase in their lifetimes.

Surface behavior of a model surfactant: a theoretical simulation study.

A quantum mechanics (QM) method has been used to calculate molecular properties of sodium dodecylbenzenesulfonate (SDBS) in vacuum and in solution. Furthermore, molecular dynamics (MD) simulations have been used to determine the dynamic behavior of SDBS moving from the bulk solution to the air/water interface. QM calculations suggest that two head-group oxygen atoms on each surfactant molecule interact with a Na(+) ion, despite the availability of three oxygen atoms in the head group.

Mechanism study of the gold-catalyzed cycloisomerization of alpha-aminoallenes: oxidation state of active species and influence of counterion.

A computational study with the B3LYP density functional theory was carried out to study the reaction mechanism for the cycloisomerization of allenes catalyzed by Au(I) and Au(III) complexes. The catalytic performance of Au complexes in different oxidation states as well as the effects of the counterion on the catalytic activities has been studied in detail. Our calculations show that the catalytic reaction is initiated by coordination of the Au(I) or Au(III) catalyst to the distal double bond of allene and activation of allene toward facile nucleophilic attack, then 3-pyrroline obtained via two-step proton shift, followed by demetalation.

Electron transfers in proteins: investigations with a modified through-bond coupling model.

By integrating the merits of previous models, a modified through-bond coupling (MTBC) model is proposed in this work and shows obvious improvement compared with previous models. With the MTBC model, the dominant electron coupling pathways in the polypeptide chains were identified, where the N-H bonds were found to be essential to the electron couplings. The local structures of peptides and proteins were finely characterized by the electron couplings and decay factors since they are structure sensitive.

Theoretical investigation on triagonal symmetry copper trimers: magneto-structural correlation and spin frustration.

The mechanisms of the magnetic coupling interactions for two trigonal-bipyramid trinuclear Cu(II) complexes Cu3(mu3-X)2(mu-pz)3X3 (X = Cl and Br, respectively) and three trigonal trinuclear Cu(II) complexes Cu3(mu3-X)(mu-pz)3Cl3 (X = Cl, Br, and O) are investigated by the calculations based on density functional theory combined with broken-symmetry approach (DFT-BS). The research on the magneto-structural correlation reveals that the magnetic coupling interaction is sensitive to the Cu-(mu3-X)-Cu angle. With the Cu-(mu3-X)-Cu angle changing from 76 to 120 degrees, the magnetic coupling interaction is switched from ferromagnetic to antiferromagnetic.

Electron delocalization and charge transfer in polypeptide chains.

In this work, the electron structure and charge-transfer mechanism in polypeptide chains are investigated according to natural bond orbitals (NBO) analysis at the level of B3LYP/6-311++G**. The results indicate that the delocalization of electrons between neighboring peptide subgroups can occur in two opposite directions, and the delocalization effect in the direction from the carboxyl end to the amino end has an obvious advantage. As a result of a strong hyperconjugative interaction, the lowest unoccupied NBO of the peptide subgroup, pi*C-O, has significant delocalization to neighboring subgroups, and the energies of these NBOs decrease from the carboxyl end to the amino end.

The study of chiral discrimination of organophosphonate derivatives on pirkle type chiral stationary phase by molecular modeling.

Molecular modeling and molecular dynamics (MD) have been used to study the chiral discrimination and interaction energy of organophosphonate in N-(3,5-dinitrobenzoyl)-S-leucine chiral stationary phase (CSP). The elution order of the enantiomers can be predicted from the interaction energy. Quantitative structure-retention relationship (QSRR) has also been used as an alternative method to confirm the elution order of enantiomers.

Magnetic interactions in two heterobridged dinuclear copper(II) complexes: orbital complementarity or countercomplementarity?

The mechanisms of magnetic exchange interactions in two heterobridged mu-hydroxyl-mu-X dicopper complexes A and B (X = azaindole for A and X = pyrazole for B) are investigated by the calculations based on density functional theory combined with the broken-symmetry approach (DFT-BS). It is found that although the coordination circumstances of the copper centers in the two complexes are very similar, the magnetic magnitudes and signs are diametrically opposed. By the theoretical analyses of magnetic orbital interaction and spin distribution, it is indicated that the difference between the magnetic properties of the two complexes is due to the distinction of orbital interaction of two bridge ligands.

DFT description on electronic structure and optical absorption properties of anionic S-doped anatase TiO2.

Plane-wave-based pseudopotential density functional theory (DFT) calculations are used to characterize the doping effect of S substituting for O in anatase TiO(2). Through band structure calculation, a direct band gap is predicted in TiO(2)(-)(x)S(x). Electronic structure analysis shows that the doping S could substantially lower the band gap of TiO(2) by the presence of an impurity state of S 3p on the upper edge of the valence band.

Theoretical elucidation on the antioxidant mechanism of curcumin: a DFT study.

[reaction: see text] Bond dissociation enthalpies (BDEs) for the curcumin-related compounds have been calculated using density functional theory (DFT) methods. It was found that the antioxidant mechanism of curcumin was a H-atom abstraction from the phenolic group, not from the central CH2 group in the heptadienone link. Curcumin, methylcurcumin, and half-curcumin had similar O-H BDEs, indicating that the two phenolic groups in curcumin were independent of each other.