Heterocycle compounds synthesized by amide ligand-promoted copper salt catalyzed construction of C-O(S) bonds.

We introduce a mild method for the ligand-promoted copper-catalyzed coupling of 2-halophenol to construct DBDO using cost-effective copper salts, ligands, and alkaline reagents. This method cleverly makes 2-bromophenol complete the Ullman reaction twice, achieves efficient C-O(S) bond coupling and intermolecular cyclization, and yields high amounts of oxygen(sulfur)-containing six-membered ring products. Less reactive 2-chlorophenol was also applied in this catalytic system. The application range of the copper-amide catalytic system was further expanded. Moreover, the success of a gram-scale reaction demonstrated that this operationally simple process is scalable.

Cobalt-Graphene Catalyst for Selective Hydrodeoxygenation of Guaiacol to Cyclohexanol.

Herein, cobalt-reduced graphene oxide (rGO) catalyst was synthesized with a practical impregnation-calcination approach for the selective hydrodeoxygenation (HDO) of guaiacol to cyclohexanol. The synthesized Co/rGO was characterized by transmission electron microscopy (TEM), high-angle annular dark-field scanning TEM (HAADF-STEM), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, X-ray diffraction (XRD), and H2 temperature-programmed reduction (H2-TPR) analysis. According to the comprehensive characterization results, the catalyst contains single Co atoms in the graphene matrix and Co oxide nanoparticles (CoOx) on the graphene surface. The isolated Co atoms embedded in the rGO matrix form stable metal carbides (CoCx), which constitute catalytically active sites for hydrogenation. The rGO material with proper amounts of N heteroatoms and lattice defects becomes a suitable graphene material for fabricating the catalyst. The Co/rGO catalyst without prereduction treatment leads to the complete conversion of guaiacol with 93.2% selectivity to cyclohexanol under mild conditions. The remarkable HDO capability of the Co/rGO catalyst is attributed to the unique metal-acid synergy between the CoCx sites and the acid sites of the CoOx nanoparticles. The CoCx sites provide H while the acid sites of CoOx nanoparticles bind the C-O group of reactants to the surface, allowing easier C-O scission. The reaction pathways were characterized based on the observed reaction-product distributions. The effects of the process parameters on catalyst preparation and the HDO reaction, as well as the reusability of the catalyst, were systematically investigated.

Experimental and modeling investigation of organic modified montmorillonite with octyl quaternary ammonium salt.

The sodium montmorillonite was organic modified with three kinds of quaternary ammonium salts containing 1 to 3 octyl chains, and then the organic montmorillonite was studied by FT-IR, XRD, and TG characterization as well as Monte Carlo simulations, to explore the influence of the number of octyl chains and the loading of intercalated cations on the basal spacing (d001) of the modified montmorillonite complexes. According to the distribution of intercalated quaternary ammonium cations and the energy change of the montmorillonite complexes, a reasonable explanation was given for the enlargement of the interlayer space. The results of experimental characterization and Monte Carlo simulations show that all the three intercalation agents can enlarge the interlayer space of montmorillonite complexes. The more the number of octyl chains in the salt, the more significant expanding effect on the interlayer space. The three intercalation cations exhibited a distribution arranged from mono-layered to multi-layered structure as the loading of intercalated cations increases.

Polarizable TIP7P Water Model with Perturbation Charges Evaluated from ABEEM.

A polarizable version of the rigid seven-site (TIP7P) water model with the atom-bond electronegativity equalization method (ABEEM) is proposed. The model uses direct polarization, where an isolated water monomer in the equilibrium geometry is assumed as a reference state and the polarization of the monomer arises from interacting with other molecules as a perturbation of the reference state. The charge on each site of the monomer splits into reference charge and perturbation charge. The perturbation charge arises only because of other reference charges. The interaction of the perturbation charge with other perturbation charges is replaced using polarization scaling to enhance the interaction of perturbation charge with the reference charges of the sites from other molecules. The perturbation charges are updated by evaluating explicit expressions once. This direct polarization is time-reversible because the charge update is independent of the charges in previous simulation steps. A Slater-type damping function moderates the short-range electrostatics to treat charge diffusion. The Ewald method corrects the long-range electrostatics both in the nuclei movement and in electronegativity equalization to diminish the size effect. The water model is parameterized by fitting the ab initio results of water clusters and the experimental results of water monomers and thermodynamic properties for liquid water. Owing to polarizability, the model performs better than the TIP7P model in terms of vaporization enthalpy, isothermal compressibility, and shear viscosity of the liquid phase. It performs better at the melting point of ice but slightly worse under critical conditions than the TIP7P model. Direct polarization has a low time complexity of O(N) and is a good choice for ABEEM to improve its computational efficiency.

Seven-Site Effective Pair Potential for Simulating Liquid Water.

Constant pressure simulations were carried out to construct a new rigid nonpolarizable seven-site water model (TIP7P), which is an effective and efficient version of flexible seven-fluctuating-charge water model. In this model, the positive charges are located on three nuclei and the negative charges disperse on two bond sites at the geometric center of each OH bond and two lone-pair sites along the tetrahedral direction away from the oxygen atom. Our new model performs better than other models in properties, such as radial distribution function, liquid density, thermal expansion coefficient, isothermal compressibility, vaporization enthalpy, isobaric heat capacity, static dielectric constant, self-diffusion coefficient, critical temperature, and density. This model reproduces liquid density and static dielectric constant over the temperatures from 253 to 373 K at 1 atm with the standard deviation of 0.0010 g/cm3 and 1.37 to the experimental data, respectively. The maximum density is 1.0006 g/cm3 at 277 K. The calculated isobaric compressibility presents a minimum at about 310 K close to the experimental value of 319 K. The self-diffusion coefficient agrees the experimental data with the standard deviation of 0.55 × 10-5 cm2/s, although it is not the target property for parameterization. Liquid-vapor phase equilibrium was examined in slab simulations. The evaluated critical temperature and density are 633 K and 0.337 g/cm3 close to the experimental values of 647.096 K and 0.322 g/cm3. This model also presents reasonable vaporization enthalpy and isobaric heat capacity. Based upon good performances mentioned, our new model is a good choice for more accurate investigation to large molecular systems.

Computational and experimental research on mechanism of cis/trans isomerization of oleic acid.

The harm of trans-fatty acids to health has aroused public concern. It is believed that the main source of trans-fatty acids in diets is the isomerization of unsaturated fatty acids in edible oils during cooking. However, the information on the isomerization mechanism is very limited. In this paper, we used oleic acid, an unsaturated fatty acid, as a simplified model for edible oil and investigated the mechanism of cis/trans isomerization by computation and experiments. The computational results show that Rc-O-O-H is a very important intermediate, and the cleavage of O-O bond in Rc-O-O-H is the rate-controlling step during the cis/trans isomerization. Using the ATR-FTIR measurements, the contents of elaidic acid were measured quantitatively in sites. The experimental results indicate that the cis/trans isomerization of oleic acid can occur obviously only under oxidizing condition when the temperature is higher than 120 °C.

Reaction Mechanism of 4-Chlorobiphenyl and the NO3 Radical: An Experimental and Theoretical Study.

Experiment and theoretical chemistry calculations were conducted to elucidate the mechanism of the reaction between 4-chlorobiphenyl (4-CB) and the NO3 radical. The degradation of PCBs was investigated mechanistically through transient absorption spectroscopy technology and high-accuracy theoretical calculation by using 4-CB as the model. Laser flash photolysis (LFP) experiments were performed at 355 nm. The main intermediate was analyzed through transient absorption spectroscopy and identified to be a charge transfer complex (CTC). The final products were identified through GC-MS analysis. The ground states and excited states of the reactants were calculated through density functional theory (DFT) method. The absorption bands at 400 and 700 nm show good agreement with the experimental results. The ratio of absorbance at 400 and 700 nm is 1.6, and the experimental value is 1.8. Analysis of the charge population indicated that one unit charge transfer from 4-CB to NO3. The entire reaction process was divided into two phases. In the first phase, the CTC intermediate was formed by electrostatic attraction between 4-CB and the NO3 radical. In the second phase, the most important channel of subsequent reactions is the σ-complex as an intermediate formed by N-C coupling. The final product 4-chloro,2-nitrobiphenyl was generated with the breakage of BC-H and BN-O, and benzene derivatives were formed by other channels.

Investigation of Transport Properties of Water-Methanol Solution through a CNT with Oscillating Electric Field.

Molecular dynamics simulations were used to investigate the transport properties of water-methanol solution getting through a carbon nanotube (CNT) with an oscillating electric field. Eight alternating electric fields with different oscillation periods were used in this work. Under the oscillating electric field, water molecules have the advantage of occupying a CNT over methanol molecules. Meanwhile, the space occupancy of water-methanol solution in the CNT increases as the oscillating period increases. More importantly, we found that the oscillating period of electric field affects the van der Waals interaction of the solution inside the CNT and the shell of the CNT, which results in the change in the number of hydrogen bonds in the water-methanol solution confined in the CNT. And the change in the hydrogen-bond network leads to the change in transport properties of water-methanol solution.

Experimental and theoretical studies on compositions, structures, and IR and NMR spectra of functionalized protic ionic liquids.

The compositions and structures of amine-based functionalized protic ionic liquids (PILs), namely N,N-dimethyl(cyanoethyl)ammonium propionate (DMCEAP) and N,N-dimethyl(hydroxyethyl)ammonium propionate (DMEOAP) have been investigated systematically by IR and (1)H NMR spectroscopy and density functional theory (DFT) calculations. Analysis of the IR spectra suggests that both DMCEAP and DMEOAP are composed of neutral and ionized species in the liquid phase, the former one mainly existing in the state of precursor molecules, and the latter mainly as ion-pairs. The ratio of precursor molecules to ion-pairs in the liquid phase depends on the types of precursors, especially the functional groups of cations. (1)H NMR spectra indicate that there is a dynamic equilibrium between the neutral and ionized species, probably due to the formation of some intermediates in the PILs. The DFT calculations have been carried out to reveal the conformation, and obtain the corresponding IR and (1)H NMR spectra of the neutral and ionized species, so that the theoretical support to the experimental results can be provided. The present study will help understand the properties of PILs and provide guidance for further applications of PILs.

[DFT/TDDFT study on the structure and absorption spectra of free base, N-/neo-confused porphyrin].

Porphyrin is an important class of photochemical materials, which has been widely used in various fields. Computational investigations into the ground state structures and orbital energy levels of free base porphyrin (FBP), neo-confused porphyrin (NECP) and N-confused porphyrin (NCP) were performed with density functional theory(DFT). Absorption spectra were calculated at TD-B3LYP/6-31+G(d). Degeneracy of HOMO and HOMO-1 is lost, which would account for the shoulder peaks about the most intense transitions of FBP and NECP. Following FBP, NECP and NCP order, the orbital energy level (OEL) of LUMO decreases while the OEL of HOMO increases, which lead to the red shift of adsorption spectra. The energy difference between LUMO and LUMO+1 is almost the same as the difference between HOMO and HOMO-1, which would account for the only most intense transition of NCP. Solvent effect on ground state structures and absorption spectra was also investigated. The data shows that the character peak of Soret band and Q band changes in different solvent (benzene, chloroform, acetonitrile and water). So we further focus on discussing the N atom position and solvent effects on the energy level and Soret/Q bands of FBP, NCP and NECP, as well as clarifying its variation regularity and mechanism.

Comparative molecular dynamics simulations of histone deacetylase-like protein: binding modes and free energy analysis to hydroxamic acid inhibitors.

Histone deacetylases (HDACs) play an important role in gene transcription, and inhibitors of HDACs can induce cell differentiation and suppress cell proliferation in tumor cells. Histone deacetylase1 (HDAC1) binds suberanilohydroxamic acid (SAHA) and 7-phenyl-2, 4, 6-hepta-trienoyl hydroxamic acid (CG-1521) with moderately low affinity (DeltaG = -8.6 and -7.8 kcal mol(-1)). The structurally related (E)-2-(3-(3-(hydroxyamino)-3-oxoprop-1-enyl)phenyl)-N(1),N(3)-diphenylmalonamide (SK-683), a Trichostatin A (TSA)-like HDAC1 inhibitor, and TSA are bound to the HDAC1 with -12.3 and -10.3 kcal mol(-1) of DeltaG, higher binding free energies than SAHA and CG-1521. Histone deacetylase-like protein (HDLP), an HDAC homologue, shows a 35.2% sequence identity of HDLP and human HDAC1. Molecular dynamics simulation and the molecular mechanics/generalized-Born surface area (MM-GBSA) free energy calculations were applied to investigate the factors responsible for the relatively activity of these four inhibitors to HDLP. In addition, computational alanine scanning of the binding site residues was carried out to determine the contribution components from van der Waals, electrostatic interaction, nonpolar and polar energy of solvation as well as the effects of backbones and side-chains with the MM-GBSA method. MM-GBSA methods reproduced the experimental relative affinities of the four inhibitors in good agreement (R(2) = 0.996) between experimental and computed binding energies. The MM-GBSA calculations showed that, the number of hydrogen bonds formed between the HDLP and inhibitors, which varied in the system studied, and electrostatic interactions determined the magnitude of the free energies for HDLP-inhibitor interactions. The MM-GBSA calculations revealed that the binding of HDLP to these four hydroxamic acid inhibitors is mainly driven by van der Waals/nonpolar interactions. This study can be a guide for the optimization of HDAC inhibitors and future design of new therapeutic agents for the treatment of cancer.

Theoretical study on the motion of a La atom inside a C82 cage.

The motion of a single lanthanum atom inside a C82 (C2v) fullerene cage has been investigated by means of the hybrid density functional method (B3LYP). The obtained potential energy surface (PES) suggests that the encapsulated La atom can oscillate only around the minimum energy potential well, which is apparently different from the scenario of a giant bowl-shaped movement at room temperature described by Nishibori et al. (Nishibori, E.; Takata, M.; Sakata, M.; Tanaka, H.; Hasegawa, M.; Shinohara, H. Chem. Phys. Lett. 2000, 330, 497-502.) Interestingly, our calculations show that the La atom may probably undergo a boat-shaped movement when the temperature is high enough. In addition, the computed 13C NMR spectrum of the C2v [La@C82]- is in an excellent agreement with the experimental nuclear magnetic resonance (NMR) spectrum (Tsuchiya, T.; Wakahara, T.; Maeda, Y.; Akasaka, T.; Waelchli, M.; Kato, T.; Okubo, H.; Mizorogi, N.; Kobayashi, K.; Nagase, S. Anew. Chem. 2005, 117, 3346-3349), which confirms that the isomer of La@C82 with the C2v symmetry is the most stable.

Proton transfer in nanoconfined polar solvents. 1. Free energies and solute position.

The reaction free energy curves for a model phenol-amine proton-transfer system in a confined CH3Cl solvent have been calculated by Monte Carlo simulations. The free energy curves, as a function of a collective solvent coordinate, have been obtained for several fixed reaction complex radial positions (based on the center-of-mass). A smooth, hydrophobic spherical cavity was used to confine the solvent, and radii of 10 and 15 A have been considered. Quantum effects associated with the transferring proton have been included by adding the proton zero-point energy to the classical free energy. The results indicate the reaction complex position can be an important component of the reaction coordinate for proton-transfer reactions in nanoconfined solvents.