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. It is suggested that doping BNNTs with Fe is an available strategy for improving the properties of BNNTs, and that Fe-doped BNNT would be a potential resource for adsorbing PCP pollutant in environments.

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. Since the π-π stacking interaction between the two pyrene molecules was very weak, formation of the excimer was a dynamic process with the two pyrene molecules alternately separating and associating with each other. In this case, the two pyrene molecules were found to be mainly distributed in the palisade layer of the micelle due to the balance between the weak π-π stacking interaction and the hydrophobic interaction of probe molecules with the surfactant tails.

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. Our calculation indicates that these four pathways have high barriers and a small energy gap between two more favorable R and S pathways. We have analyzed the effects of the TFA anion and H(2)O on the activity and enantioselectivity of catalytic epoxidation. It is found that the TFA anion acts as a counterion to stabilize the transition states of the catalytic epoxidation by hydrogen-bond acceptance, leading to decreases in the barriers of the nucleophilic addition and ring-closure processes. The most significant decrease occurred in the ring-closure step of the Z-R-pathway, resulting in H-bond-induced enantioselectivity. Our calculations also show that water cooperates with TFA to further increase the reaction rate significantly.

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. We report the changes of the structure of the six SAMs with different surfaces in the presence of water, and the area of the wetted surface of each SAM, depending on the terminal group. Our results suggest that a corrugated and hydrophobic surface will be formed if the headgroups of SAM surface are not able to form H-bonds either with water molecules or between adjacent groups. In contrast, the formation of hydrogen bonds not only among polar heads but also between polar heads and water may enhance the SAM surface hydrophilicity and corrugation. We explicitly discuss the micromechanisms for the hydration of three hydrophilic SAM (CN-, NH(2)- and COOH-terminated) surfaces, which is helpful to superhydrophilic surface design of SAM in biomimetic materials.

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. The divalent ions can screen the interaction between the polar head and Na(+) ions. Thus, Ca(2+) ions locate near the vapor/liquid interface to bind to the headgroup, making the aggregations much more compact via the salt bridge. The potential of mean force (PMF) between Ca(2+) and the headgroups shows that the interaction is decided by a stabilizing solvent-separated minimum in the PMF. To bind to the headgroup, Ca(2+) should overcome the energy barrier. Among contributions to the PMF, the major repulsive interaction was due to the rearrangement of the hydration shell after the calcium ions entered into the hydration shell of the headgroup. The PMFs between the headgroup and Ca(2+) in the SDSn systems showed higher energy barriers than those in the SDC systems. This result indicated that SDSn binds the divalent ions with more difficulty compared with SDC, so the ions have a strong effect on the hydration shell of SDC. That is why sulfonate surfactants have better efficiency in salt solutions with Ca(2+) ions for enhanced oil recovery.

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. According to the analyses of the magneto-structural correlation, it is revealed that the magnetic coupling interaction switches from ferromagnetic to antiferromagnetic at the point of the bridging angle Mn-(µ-OCH(3))-Mn = 99°, which is equal to the value in the origin crystal. Significant correlation between the magnetic properties and the component of the d orbitals in these systems shows that the larger contribution of the d(z(2)) orbital corresponds to the larger ferromagnetic coupling interaction. These results should provide a means to control the magnetic coupling of the polynuclear Mn systems, which is instructive for the design of new molecular magnetic materials.

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. In the second hydration shell around the headgroup, additional water molecules are bound to the headgroup oxygen atoms either directly or bridged by Ca(2+) and Mg(2+). The PMF shows that the energy barriers to ion-pairing between the headgroup and Ca(2+) and Mg(2+) in the SDSn system are higher than those in the SDS system, and the water coordination numbers for Ca(2+) or Mg(2+) in SDS solution are lower. This result indicates that SDS binds the ions easily compared with SDSn, and the ions have a strong effect on the original hydration structure. That is why sulfonate surfactants such as SDSn have better efficiency in salt solution with Ca(2+) and Mg(2+) for enhanced oil recovery.

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. MD simulations showed that the Na(+) ion must overcome the energy barrier between two solvent layers around the head group to form stable ion pair in solution, which is consistent with experimental results. In the simulation, in moving from the bulk to the interface, SDBS can aggregate in a short time, and the adsorption adopts a preferred orientation. The results indicate that formation of favorable hydrophobic interactions of the surfactant alkyl chains is the origin of interfacial adsorption of SDBS.

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. On the basis of our calculations, H shifts are key steps of the catalytic cycle, which are significantly affected by the gold oxidation state, counterion, ligands, and assistant catalyst. AuCl is found to be more reactive than AuCl(3); however, the Au(III)-catalyzed path does not involve an oxidation state change from Au(III) to Au(I). Our calculated results rationalize the experimental findings well and overthrow the previous conjecture about Au(I) serving as the catalytically active species for Au(III)-catalyzed cycloisomerization.

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. The neighboring carbonyl O-O distances are qualitatively correlated with the decay factors, and the deviations from the transconfigurations will weaken the coupling interactions. When the two amino acids being studied are not close in sequence, the couplings through hydrogen bonds are probably the main pathway because the electron transfers in this way save many steps, albeit the decay factor is less than that of per bond, consistent with the classical electron-tunneling model developed by Beratan [Science 252, 1285 (1991)]. It was found that the MTBC model can be effectively extended to study the electron transfers in complex biological systems with the combination of the fragment approach, which takes into account the contributions of key hydrogen bonds.

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. According to the analysis of the molecular orbitals and the variation of the spin-state energies versus the ratio of the magnetic coupling constants, it is found that there exists spin frustration phenomenon in these complexes.

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 formation of intramolecular O...H-N type hydrogen bonds also helps to delocalize the electron from the carboxyl end to the amino end. Thus, the electron will flow to the amino end. The superexchange mechanism is suggested in the electron-transfer process.

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. Owing to the lack of side chains, various types of hydrogen bonding interactions are detected in the glycine residues. The conformational analyses of proteins are mainly based on the dihedrals. Theta(1)( angleH(5)C(2)C(3)O(4)), Theta(2)( angleH(6)C(2)C(3)O(4)) and Theta(3)( angleN(1)C(2)C(3)O(4)) are the three key dihedrals to determine the glycine conformations, which were found to change synchronously and correlate with each other by four linear equations. It thus provided the first evidence of the correlation of intra-dihedrals for the amino acid residues in proteins. In addition, the three dihedrals of the gas-phase glycine conformations were also found to suit well with these linear equations, elucidating the rationality of using amino acids as the computational models of proteins.

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. Namely, the weak ferromagnetic coupling for complex A arises from the orbital countercomplementarity of the hydroxo and azaindole bridges while the strong antiferromagnetic coupling for complex B arises from the orbital complementarity of the hydroxo and pyrazolato bridges.

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. Molecular mechanics (MM), molecular dynamics and QSRR proved to be useful methods to study chiral discrimination.

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.