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α-Fe2O3/Ni-Based Thin Film Electrocatalytic Interface for Photoelectrochemical Water Oxidation

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Active sites of heterogeneous nucleation understood as chemical reaction sites

The role of active sites in heterogeneous nucleation can be understood on the basis of chemical thermodynamics as chemical reaction sites. The basic assumption is the formation of a chemical bond between the atoms (or molecules) of the nuclei with the atoms (or molecules) of the active site. This view on nucleation will be applicable to all cases where the nucleating phase has a sufficient chemical affinity to the active site.

Environmentally Friendly Fabrication of Surface‐Modified MWNT‐Supported Pt Nanocomposites for PEMFCs

AbstractThe functionalisation process of carbon nanotubes (CNTs) is required as a primary step in fabricating CNTs‐supported composites. In this study, multiwall carbon nanotubes (MWNTs) were treated under N2 atmospheric pressure plasma in order to functionalise their sidewalls with nitrogen‐containing and other functional groups. The surface‐treated MWNTs with –NO, –NH2 and other functional groups grafted on their sidewalls were analysed by X‐ray photoelectron spectroscopy (XPS). In addition, a certain amount of structural disorder generated by the continuous decoration of functional groups on the MWNT sidewalls was investigated by Raman spectroscopy and high‐resolution transmission electron microscopy (TEM). The functional groups introduced by N2 atmospheric pressure plasma were used as the chemical reaction sites for fabricating the Pt/MWNT nanocomposites. The deposition manner of Pt nanoparticles from their precursor ions (PtCl2–6) was positively correlated with the proportion of the surface functional groups. The plasma‐treated MWNT‐supported platinum catalysts exhibited higher electrochemical activity for hydrogen adsorption/desorption and methanol oxidation than did the catalysts prepared with MWNTs treated by HNO3/H2SO4. These results were due to the uniformly deposited Pt nanoparticles on the MWNTs caused by the strong interactions between the Pt precursors and the functional groups formed by N2 atmospheric pressure plasma.

The evolutions of the structure stability, vibrational frequency, frontier orbital, and electronegativity of the unconventional exohedral fullerenes C 64X 4 (X = H, F, Cl, Br, and I): A density functional study

The density functional theory is employed to analyze the evolutions of the structural and electronic properties of the unconventional carbon halogen molecules C 64X 4 (X = F, Cl, Br, and I). It is found that the evolutions of the bond dissociation energies, the energy gaps, and the maximal frequencies all decrease with the increased atomic number of X, indicating that the stabilities should decrease from C 64F 4 to C 64I 4. C 64X 4 (X = F and Br) could be isolated and synthesized due to the successful isolation of C 64Cl 4 by Han et al. [X. Han, S.J. Zhou, Y.Z. Tan, X. Wu, F. Gao, Z.J. Liao, R.B. Huang, y.q. Feng, X. Lu, S.Y. Xie, L.S. Zheng, Angew. Chem. Int. Ed. 47 (2008) 5340]. It is revealed from analyzing the frontier orbitals of C 64 that the C–C bonds locate on the pentagon–pentagon fusions function as active sites in chemical reactions, facilitating hydrogen atoms or halogen atoms attachment. The electronegativity of C 64X 4 cluster molecules decrease with the increased atomic number of X, however, the electronegativity of the CX fragment in the molecules is affected by its located site. The molecule electronegativity χ and the chemical hardness η of C 64X 4 (X = F, Cl, Br, and I) decrease with the increased atomic number of X, while the electrophilicity index ω increases from C 64F 4 to C 64I 4. The C 3 v –C 64 is weak aromatic, whereas, the C 64X 4 (X = F, Cl, Br, I) show nonaromatic character.

Electronic Structure of Unsaturated V2O5(001) and (100) Surfaces: Ab Initio Density Functional Theory Studies

Vanadium oxides based materials are well known to play an active role as catalysts in many chemical processes of technological importance like for example hydrocarbon oxidation reactions or selective catalytic reduction of NO x in the presence of ammonia. Usually the (010) surface is pointed out as the most important, however one has to underline that other low-indices surfaces are by far less studied. In the present study the electronic structure of V2O5(001) and (100) surfaces are determined by ab initio DFT methods using gradient-corrected RPBE exchange-correlation functional. As models of surface sections different embedded V14O45H20, V14O44H18, and V21O65H25 clusters are considered for the (001) surface and V12O40H20, V14O46H22, V16O52H24 for the (100) surface. Detailed analyses of the electronic structure of each cluster are performed using charge density distributions, Mayer bond orders, electrostatic potential maps, character of frontier orbitals, and density of states (total as well as partial, atom projected). Results of the calculations show that overall negative charge of the surface oxygen sites scales with their coordination independent of the surface orientation. Terminal oxygen O(1) is charged the least negatively while doubly coordinated atoms –O(2) and Oe(2) have charge twice as large. This indicates that bridging (for (001) and (100) netplanes) and edging (only for (001) netplane) oxygen sites are more nucleophilic than terminal vanadyl sites, which becomes important in view of the reactivity of the different sites for surface chemical reactions. Vanadium atoms present at these surfaces are positively charged (electrophilic) and may play a role of electron acceptors. The unsaturated surfaces show a strong tendency to surface relaxation that manifest by large relaxation energies.

Determination of active sites based on unified analysis of potential energy profile in chemical reaction: Application to C–H activation of methane by Ti(IV)-imido complex

This study presents a simple and quantitative scheme to determine the active sites in chemical reactions. We first introduce a novel index for characterizing the potential energy profiles in the reactions. Next, the energy density analysis is applied to expand the energy differences of the reactant or the product with respect to the transition state. By setting the threshold for the differences, one can extract the active sites, in which greater energetic changes happen in the reactions. Numerical applications, performed for the C–H activation of methane by a Ti(IV)-imido complex, have confirmed the usefulness of the present scheme.

Subdiffraction Far-Field Imaging of Luminescent Single-Walled Carbon Nanotubes

Far-field near-infrared fluorescence microscopy of single-walled carbon nanotubes (SWNTs) has been hampered by the diffraction limit to resolution. A new analysis method is presented that allows subwavelength (<lambda/10) mapping of single-molecule chemical reaction sites on semiconducting SWNTs, enabling precise localization of excitonic luminescence regions along the nanotube axis through a nonperturbing, far-field optical measurement. This method is applied to reveal the subdiffraction lengths, curvatures, and defects of luminescent SWNTs in unprecedented detail.

Vibrational exciton coupling in pure and composite sulfur dioxide aerosols

Icy aerosol particles determine weather processes in planetary atmospheres and are discussed as sites of chemical reactions in interstellar dust. One of the interesting ice systems in this context are pure and composite SO2 particles. Vibrational exciton coupling is exploited in the present study to understand the properties of SO2 aerosol particles from their infrared spectroscopic signatures. The condensation to pure SO2 ice particles leads to a partially amorphous structure of the particles, whose infrared spectra do not show pronounced shape effects. The simultaneous condensation of SO2 and CO2 gas results in aerosol particles with a core-shell structure. Icy SO2 forms the core, whereas CO2 remains in the shell. This structure is mainly determined by the different thermodynamic properties of the two substances and the less favorable intermolecular interactions between SO2 and CO2 compared with the pure substances. The example of mixed sulfur dioxide/ammonia particles demonstrates that nanosized aerosol particles are ideal nanoreactors. They facilitate an easy homogeneous mixture of the reactants providing an interface-free reaction environment.

Facile approach to functionalizing polymers with specific chemical groups by an ozone treatment: Preparation of crosslinkable poly(vinylidene fluoride) possessing benzoxazine pendent groups

A facile method for modifying a polymer with specific chemical groups was conducted through the incorporation of hydroxylbenzene groups into an ozone-treated polymer. The hydroxylbenzene pendent groups on the functionalized polymer provided reactive sites for further chemical reaction and modification. A poly(vinylidene fluoride) possessing benzoxazine pendent groups (PVDF-Bz) was prepared to demonstrate this polymer modification. The performance of the polymer functionalization and chemical structure characterization were determined with Fourier transform infrared, 1H NMR, ultraviolet–visible spectroscopy, and elemental analysis. PVDF-Bz was a crosslinkable polymer, and the crosslinked poly(vinylidene fluoride) exhibited improved mechanical properties.

Density Functional Theory in Transition-Metal Chemistry: A Self-Consistent HubbardUApproach

Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on generalized-gradient approximations often fail to describe energetics, multiplet structures, reaction barriers, and geometries around the active sites. We suggest here an alternative approach, derived from the Hubbard U correction to solid-state problems, that provides an excellent agreement with correlated-electron quantum chemistry calculations in test cases that range from the ground state of Fe2 and Fe2- to the addition elimination of molecular hydrogen on FeO+. The Hubbard U is determined with a novel self-consistent procedure based on a linear-response approach.

Ab initio studies on the molecular electrostatic potential of C 50

Ab initio quantum chemical methods at the HF/6-31G* and MP2/6-31G* levels of theory were applied to the investigation of the relative stability of two fullerene isomers of C 50. Full geometry optimization of the systems was carried out and the electrostatic potential distributions were calculated. The effect of the electron correlation on the electrostatic potential distribution of C 50 isomers was analyzed. The calculated results show that potential minima V min( r) inside the sphere occur at the center of the sphere. The largest regions with the most negative MEP outside the sphere are localized in the neighborhood of pentagon–pentagon vertex fusions. They constitute most probably the active sites in chemical reactions. The present results might offer a more reasonable explanation for protonation and alkylation of C 50 fullerene.

Effect of oriented or random PEGylation on bioactivity of a factor VIII inhibitor blocking peptide

Peptides as therapeutic substances are efficient agents in the treatment of several diseases. However, they often have to be chemically modified in order to be suited as therapeutic agent. Conjugation to large carrier molecules is often required. A critical step is the identification of available sites for chemical reaction, without influencing bioactivity. Peptide 238/S1 with the sequence NH(2)-PYWKWQYKYD-COOH previously selected from a combinatorial decapeptide library, has the ability to block inhibitory antibodies against blood clotting factor VIII (FVIII) and therefore, it constitutes a lead for developing a drug to treat patients suffering from development of such antibodies. The aims of this study were (i) to identify sites of the peptide, which are suited for modification without losing bioactivity and (ii) to find out the influence of molecular size of polyethylene glycol (PEG) for bioactivity of the peptide. The contribution of each amino acid residue to biological functionality was investigated by mutational analysis. This method confirmed that the N-terminus is crucial for activity, whereas both lysine residues could be exchanged by other L-amino acids. Using mutational analysis it was possible to identify peptides with higher reactivity compared to the wild type 238/S1. PEGylation experiments demonstrated that conjugation of the peptide to PEG 20,000 resulted in a loss of reactivity, while PEG 5,000 could maintain the bioactivity when conjugated in a site directed manner. The peptide lost its neutralization properties when PEG was coupled to the N-terminus, again indicating that this part of the peptide is important for functionality.

Solubility and electrical transport properties of thiolated single-walled carbon nanotubes

Single-walled carbon nanotubes have been modified using dodecanethiol as the reaction agent. The thiolated nanotubes form a stable suspension in toluene, and can be used for Langmuir-Blodgett deposition of monolayers. The nanotube conductance decreases by three orders of magnitude and acquires a gate dependence with a memory effect. The conductance for the on and off states with 0V applied to the gate differs by more than two orders of magnitude. These effects are explained in terms of a chemical reaction between the tube wall and the thiol. The thiolation process is also observed on the exposure of the nanotubes to toluene solutions of dodecanethiol-stabilized Au nanoparticles. The nanoparticles can thus be used for labeling or manipulating the location of the chemical reaction sites on the tube wall. The reaction is followed using optical-absorption measurements.

Theoretical study on fulvic acid structure, conformation and aggregation: A molecular modelling approach

The ubiquitous presence of humic substances (HS), combined with their ability to provide multiple sites for chemical reaction, makes them relevant to numerous biogeochemical processes such as mineral weathering, nutrient bioavailability, and contaminant transport. The reactivity of HS depends on their functional group chemistry and microstructure, which are in turn influenced by the composition of the surrounding media. In order to help towards an understanding of structure conformations and aggregation process of HS in soils and waters and to get a better knowledge of these kinds of materials, a fulvic acid (FA) has been modelled as a function of its ionic state under different conditions. Our proposed theoretical model based on the Temple-Northeastern-Birmingham (TNB) monomer fits well with experimental observations on the solubility (dipolar moment) and electronic and vibrational spectra of FAs. The presence of water molecules has a great stabilization effect on the electrostatic energy; this effect is greater as ionized rate increases. In vacuum, the non-ionized aggregated species are more stable than monomers because of the increase in their interaction due to H-bonding and non-bonding forces. When the molecules are ionized, no aggregation process takes place. In solution, the FA concentration is a critical factor for the aggregation. The system containing two FA molecules probably did not form aggregates because its equivalent concentration was too low. When the concentration was increased, the system gave rise to the formation of aggregates. The ionic state is another critical factor in the aggregation process. The ionized FA has a higher electric negative charge, which increases the energetic barriers and inhibits the approximation of FA caused by the Brownian movement.

The stabilization of supported gold clusters by surface defects

The chemical and electronic properties of surfaces to a large extent are controlled by defects. Defects facilitate the adsorption of gases and serve as reactive sites for chemical reactions. Furthermore, surface defects are a key to the nucleation, growth, and stability of metal clusters on metal oxide surfaces. This paper summarizes recent studies to assess the role of defects on Au cluster nucleation, growth, and stability on SiO 2 and mixed TiO x –SiO 2 thin films. For a SiO 2 thin film, Au clusters sinter at elevated temperatures and pressures; however, introduction of defects on a SiO 2 surface as TiO x islands or as substitutional Ti dramatically decreases the rate of Au cluster sintering.

Properties of Fullerene[50] and D5h Decachlorofullerene[50]: A Computational Study

Stimulated by the recent preparation and characterization of the first [50]fullerene derivative, decachlorofullerene[50] (Science 2004, 304, 699), we have performed a systematic density functional study on the electronic and spectroscopic properties of C(50), its anions and derivatives such as C(50)Cl(10) and C(50)Cl(12). The ground state of C(50) has D(3) symmetry with a spheroid shape, and is highly aromatic; the best D(5h)C(50) singlet is nonaromatic. Both D(3)() and D(5h)() isomers of C(50) have high electron affinities and can be reduced easily. Due to the unstable fused pentagon structural features, C(50) is chemically labile and subject to addition reactions such as chlorination, dimerization and polymerization. The equatorial pentagon-pentagon fusions of D(5h)C(50) are active sites for chemical reactions; hence, D(5h)C(50) may behave as a multivalent group. The computed IR, Raman, (13)C NMR and UV-vis spectra of the D(5h)C(50)Cl(10) molecule agree well with the experimental data. Finally, D(5h)C(50)Cl(10) is predicted to have a high electron affinity and, hence, might serve as an electron-acceptor in photonic/photovoltaic applications. The geometry and (13)C NMR chemical shifts of C(50)Cl(12) were computed to assist further isolation experiments.

Inhibitor design by wrapping packing defects in HIV-1 proteins.

Two viral proteins, HIV-1 protease and HIV-1 integrase, have been targeted for inhibitor design to prevent assembly and maturation of HIV-1 virions. The enzymatic mechanism of these proteins involves side-chain groups that serve as general acids or bases. Furthermore, catalytic activity requires that water be removed from the microenvironment surrounding the chemical reaction site or be constrained to serve as an activated nucleophile. Here, we identify previously unrecognized structural features that promote water removal from polar catalytic regions. Packing defects in the form of hydrogen bonds that are insufficiently dehydrated intramolecularly, named "dehydrons," are strategically placed in the structure to induce an anhydrous enzymatic pathway. Dehydrons become electrostatically enhanced and stabilized upon further desolvation. Thus, packing defects act synergistically with the polar active groups to enhance the enzymatic electrostatics. However, because dehydrons are sticky, they constitute targets for inhibitor design. We noticed that inhibitors attach to polar surfaces by further desolvating dehydrons, thus blocking the active sites or the sites involved in harnessing the substrate. The dehydrons are thus required for functional reasons, making them suitable targets. The differences in success when targeting HIV-1 protease, feline immunodeficiency virus protease, and HIV-1 integrase are rationalized in terms of the dehydron distribution, revealing possible improvements in the targeting strategy. Principles of design optimization are proposed to create an inhibitor that can be neutralized only at the expense of the loss of catalytic function. The possibility of using drugs that wrap dehydrons to block protein-protein associations is also discussed.

Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimized for binding of its cognate substrates.

Natural evolution has resulted in protein molecules displaying a wide range of binding properties that include extremes of affinity and specificity. A detailed understanding of the principles underlying protein structure-function relationships, particularly with respect to binding properties, would greatly enhance molecular engineering and ligand design studies. Here, we have analyzed the interactions of an aminoacyl-tRNA synthetase for which strong evolutionary pressure has enforced high specificity for substrate binding and catalysis. Electrostatic interactions have been identified as one efficient mechanism for enhancing binding specificity; as such, the effects of charged and polar groups were the focus of this study. The binding of glutaminyl-tRNA synthetase from Escherichia coli to several ligands, including the natural substrates, was analyzed. The electrostatic complementarity of the enzyme to its ligands was assessed using measures derived from affinity optimization theory. The results were independent of the details of the calculational parameters, including the value used for the protein dielectric constant. Glutamine and ATP, two of the natural ligands, were found to be extremely complementary to their binding sites, particularly in regions seen to make electrostatic interactions in the structure. These data suggest that the optimization of electrostatic interactions has played an important role in guiding the evolution of this enzyme. The results also show that the enzyme is able to effectively select for high affinity and specificity for the same chemical moieties both in the context of smaller substrates, and in that of a larger reactive intermediate. The regions of greatest non-complementarity between the enzyme and ligands are the portions of the ligand that make few polar contacts with the binding site, as well as the sites of chemical reaction, where overly strong electrostatic binding interactions with the substrate could hinder catalysis. The results also suggest that the negative charge on the phosphorus center of glutaminyl-adenylate plays an important role in the tight binding of this intermediate, and thus that adenylate analogs that preserve the negative charge in this region may bind substantially tighter than analogs where this group is replaced with a neutral group, such as the sulfamoyl family, which can make similar hydrogen bonds but is uncharged.

Reaction of Si with HCl to Form Chlorosilanes : Time Dependent Nature and Reaction Model

We propose a chemical vapor deposition (CVD) process with closed gas recycling for making low-cost, crystalline silicon thin films for solar cells, which connects chlorosilane synthesis from Si and HCl with Si thin-film growth by CVD from chlorosilanes. In this work we studied the formation of chlorosilanes by the reaction of Si with HCl at temperatures ranging from 623 to 723 K. The reaction rate is time dependent, and many pores are formed on the surface of particles after reaction. These pores are active sites for chemical reactions, and the reaction rates increase with increasing pore area. The rate can be correlated with the conversion ratio of Si, and the temporal evolution of the reaction rate can be explained by a reaction model called the shrinking-core model with growing pores. By using this model, we estimated the reaction rates per unit area of activated surfaces and converted them into a rate equation that can be used for the reactor design. The incubation time of the reaction can be shortened by pretreating the Si particles in a fluidized bed, which probably creates defects in the native oxide layers on the particles, which in turn become reactive sites. © 2004 The Electrochemical Society. All rights reserved.

Molecular mechanism of the P-type ATPases.

The recent determination of the structure of the Ca2+-ATPase of sarcoplasmic reticulum to atomic resolution in the Ca2+-bound state and to near atomic resolution in the Ca2+-free, decavanadate-bound state has paved the way for an ultimate complete understanding of the molecular mechanism of the P-type ATPases. Analysis of this new structure information together with the large amount of biochemical information about these enzymes that preceded it has produced important new revelations about how the P-type ATPases work. Most models propose that these transporters operate by a strictly conformational energy coupling mechanism in which conformational changes in the large cytoplasmic head region mechanically drive the ions to be transported from their binding sites in the transmembrane helix region 50 A away. However, while these enzymes do indeed undergo profound conformational changes, the available evidence suggests that they do not mechanically transduce the chemical energy of ATP hydrolysis into transmembrane ion gradients via these conformational changes. As an alternative, it is proposed that the effects of the chemical events that occur at the phosphorylation/dephosphorylation site in the cytoplasmic region are exerted on the ion-binding sites via two well-defined charge transfer pathways that electronically connect the chemical reaction site with the site of ion binding. The recognition of these charge transfer pathways provides rational explanations of all of the key biochemical features of the P-type ATPase catalytic cycle. Thus, although a few details await elucidation, a nearly complete understanding of the P-type ATPase reaction mechanism may be at hand.