金属氧化物表面化学吸附和反应的量子化学簇模型方法研究

综述了本研究小组利用量子化学簇模型方法研究金属氧化物表面化学吸附和反应的工作.提出了选簇的三个原则,即电中性原则、化学配比原则和配位原则.发现在符合前两个原则的基础上,一个具有最饱和配位、或最少悬空键的簇往往是一个用于化学吸附研究的好的簇模型.与此同时,探讨了如何恰当地考虑大块固体本底的长程影响,提出了用球电荷模拟簇模型的环境、环境与簇体进行电荷自洽的SPC簇模型方法.利用该模型研究了一系列具有催化背景的重要体系,包括H2/ZnO、O/MgO、NO/MgO、N2O/MgO、N2O/Li/MgO、CO/MgO、CO/NiO等.     

Structure and stability of binary transition-metal clusters (NbCo)n (n < or = 5): a relativistic density-functional study

Equilibrium geometries and electronic properties of binary transition-metal clusters, (NbCo)n (n < or = 5), have been investigated by means of the relativistic density-functional approach. The metal-metal bonding and stability aspects of these clusters have been analyzed on the basis of calculations. Present results show that these clusters exhibit rich structural varieties on the potential-energy surfaces. The most stable structures have a compact conformation in relatively high symmetry, in which the Nb atoms prefer to form an inner core and Co atoms are capped to the facets of the core. Such building features in clustering of the Nb/Co system are related to the order of bond strength: Nb-Nb>Nb-Co>Co-Co. As the binary cluster size increases, the Nb-Co bond may become stronger than the Nb-Nb bond in the inner niobium core, which results in a remarkable increment of the Nb-Nb bond length. Amongst these binary transition-metal clusters, the singlet (NbCo)4 in T(d) symmetry has a striking high stability due to the presence of the spherical aromaticity and electronic shell closure. The size dependence of the bond length and stability of the cluster has been explored.     

Configurational Selection in Azobenzene-Based Supramolecular Systems Through Dual-Stimuli Processes

Azobenzene is one of the most studied light-controlled molecular switches and it has been incorporated in a large variety of supramolecular systems to control their structural and functional properties. Given the peculiar isomeric distribution at the photoexcited state (PSS), azobenzene derivatives have been used as photoactive framework to build metastable supramolecular systems that are out of the thermodynamic equilibrium. This could be achieved exploiting the peculiar E/Z photoisomerization process that can lead to isomeric ratios that are unreachable in thermal equilibrium conditions. The challenge in the field is to find molecular architectures that, under given external circumstances, lead to a given isomeric ratio in a reversible and predictable manner, ensuring an ultimate control of the configurational distribution and system composition. By reviewing early and recent works in the field, this review aims at describing photoswitchable systems that, containing an azobenzene dye, display a controlled configurational equilibrium by means of a molecular recognition event. Specifically, examples include programmed photoactive molecular architectures binding cations, anions and H-bonded neutral guests. In these systems the non-covalent molecular recognition adds onto the thermal and light stimuli, equipping the supramolecular architecture with an additional external trigger to select the desired configuration composition.     

Models of Molecular Structures of Al<Subscript>2</Subscript>Cr<Subscript>3</Subscript> and Al<Subscript>2</Subscript>Mo<Subscript>3</Subscript> Metal Clusters according to Density Functional Theory Calculations

The geometrical parameters of the molecular structures of aluminum–chromium and aluminum–molybdenum clusters Al₂Cr₃ and Al₂Mo₃ have been calculated by the OPBE/TZVP density functional theory (DFT) method with the Gaussian09 programL package. It has been found that each of these metal clusters can exist in twenty structural modifications, which significantly differ in stability and geometric parameters. Bond lengths and bond and torsion (dihedral) angles are reported for each of these modifications.     

Reactivities and biological functions of iron-sulfur clusters

Iron-sulfur clusters are prevalent in biological systems. Through studies of iron-sulfur proteins and synthetic model clusters, it was realized early on that these clusters functioned as facile electron transfer agents. Until recently it was widely thought that they served exclusively in that capacity. However, in the last decade, it has become clear that their reactivities and biological functions are much more diverse. It is now apparent that these clusters can serve as the active sites of enzymes, as well as in the regulation of enzymatic activity. Synthetic clusters, which have been shown to undergo a variety of core rearrangements or structural changes, have provided insight into possible mechanisms of cluster formation or activity regulation in enzymes. Rigid tripodal ligands have been constructed which capture synthetic iron-sulfur clusters in a cavity which permits controlled reactivity studies. In this article, we review these recent developments and suggest some future directions the field may take.     

A High‐Pressure Polymorph of Phosphorus Nitride Imide

Phosphorus nitride imide, PN(NH), is of great scientific importance because it is isosteric with silica (SiO₂). Accordingly, a varied structural diversity could be expected. However, only one polymorph of PN(NH) has been reported thus far. Herein, we report on the synthesis and structural investigation of the first high‐pressure polymorph of phosphorus nitride imide, β‐PN(NH); the compound has been synthesized using the multianvil technique. By adding catalytic amounts of NH₄Cl as a mineralizer, it became possible to grow single crystals of β‐PN(NH), which allowed the first complete structural elucidation of a highly condensed phosphorus nitride from single‐crystal X‐ray diffraction data. The structure was confirmed by FTIR and ³¹P and ¹H solid‐state NMR spectroscopy. We are confident that high‐pressure/high‐temperature reactions could lead to new polymorphs of PN(NH) containing five‐fold‐ or even six‐fold‐coordinated phosphorus atoms and thus rivalling or even surpassing the structural variety of SiO₂.     

Unleashing chemical power from protein sequence space toward genetically encoded “click” chemistry

We propose the concept of genetically encoded “click” chemistry (GECC) to describe the “perfect” peptide-protein reactive partners and use SpyTag/SpyCatcher chemistry as a prototype to illustrate their structural plasticity, robust interaction, and versatile applications.     

A new perspective of shape recognition to discover the phase transition of finite‐size clusters

An ultrafast shape‐recognition technique was used to analyze the phase transition of finite‐size clusters, which, according to our research, has not yet been accomplished. The shape of clusters is the unique property that distinguishes clusters from bulk systems and is comprehensive and natural for structural analysis. In this study, an isothermal molecular dynamics simulation was performed to generate a structural database for shape recognition of Ag? Cu metallic clusters using empirical many‐body potential. The probability contour of the shape similarity exhibits the characteristics of both the specific heat and Lindemann index (bond‐length fluctuation) of clusters. Moreover, our implementation of the substructure to the probability of shapes provides a detailed observation of the atom/shell‐resolved analysis, and the behaviors of the clusters were reconstructed based on the statistical information. The method is efficient, flexible, and applicable in any type of finite‐size system, including polymers and nanostructures. © 2014 Wiley Periodicals, Inc.     

Models of molecular structures of aluminum–iron clusters AlFe<Subscript>3</Subscript>, Al<Subscript>2</Subscript>Fe<Subscript>3</Subscript>, and Al<Subscript>2</Subscript>Fe<Subscript>4</Subscript> according to quantum-chemical DFT calculations

The geometrical parameters of molecular structures of three types of aluminum–iron clusters containing in total four, five, and six Al and Fe atoms in structural units have been calculated by the OPBE/TZVP density functional theory (DFT) method with the Gaussian09 program package. It has been found that the AlFe₃, Al₂Fe₃, and Al₂Fe₄ clusters can have four, eight, and nine structural modifications, which significantly differ in stability and geometric parameters. Bond lengths and bond and torsion (dihedral) angles are reported for each of these modifications.     

Intermolecular interactions in group 14 hydrides: Beyond CH···HC contacts

In line with previous work in which we established the factors that enhance attractive C?H···H?C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E?H···H?E and E···H?E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H?Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Investigation of the structural units of germanium sulfide and selenide by quantum chemical methods

This article deals with the modeling of the structural units (clusters) of germanium sulfide and germanium selenide glasses by quantum chemical (ab initio Hartree–Fock) methods. Clusters of different sizes were investigated. Geometric parameters and vibrational frequencies of these structural units were calculated. The quantum chemical calculations were followed by normal coordinate analysis. Based on the yielded results, the vibrational spectra of the clusters were simulated. The results for germanium sulfide and germanium selenide were compared. It was concluded that in the spectral regions where germanium sulfide is not applicable for fiber optics, germanium selenide or different germanium sulfide–selenides are suitable to replace it. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Binding of Reactive Oxygen Species at FeS Cubane Clusters

Reactive oxygen species (ROS) play an important role in the biochemistry of the cell and occur in degenerative processes as well as in signal transduction. Iron?sulfur proteins are particularly oxygen‐sensitive and their inorganic cofactors frequently undergo ROS‐induced decomposition reactions. As experimental knowledge about these processes is still incomplete we present here a quantum chemical study of the relative energetics for the binding of the most relevant ROS to [Fe₄S₄] clusters. We find that cubane clusters with one uncoordinated Fe atom (as found, for instance, in aconitase) bind all oxygen derivatives considered, whereas activation of triplet O₂ to singlet O₂ is required for binding to valence‐saturated iron centers in these clusters. The radicals NO and OH feature the most exothermic binding energies to Fe atoms. Direct sulfoxidation of coordinating cysteine residues is only possible by OH or H₂O₂ as attacking agents. The thermodynamic picture of ROS binding to iron?sulfur clusters established here can serve as a starting point for studying reactivity‐modulating effects of the cluster‐embedding protein environment on ROS‐induced decomposition of iron?sulfur proteins.     

Mercury,a Structural Building Block and Source of Localized Reactivity in Extended Metal–Metal Bonded Systems

Transition metal–mercury complexes were among the first compounds of study for the concept of direct metal–metal bonding which was established more than three decades ago. Since then, a large number of such systems have been synthesized and studied. The fact that mercury is readily attached to a large variety of main group or transition metals has stimulated its use as a general building block in the systematic synthesis of mixed-metal clusters. The past decade has witnessed a rapid expansion of bimetallic cluster chemistry in which species containing mercury have played a prominent role, and which has led to the discovery of many unprecedented cluster structures and reactions. In particular, the ability of mercury to form multicenter metal–metal bonds with polynuclear cluster fragments has substantially extended its coordination chemistry which was thus far dominated by simple linear structural arrangements. Although certain structural motifs are found to be common to many of the transition metal–mercury clusters investigated to date and thus enable a relatively systematic synthetic approach, the multitude of surprising discoveries has kept the interest in the chemistry of the element itself alive. The recent discovery of the redox and photochemical reactivity of some of these systems has opened up an exciting and promising area of cluster research. Its significance for the synthetic methodology lies in the fact that the increasing redox activity of molecular carbonyl clusters on going to higher nuclearities appears to set a limit on the size of metal frameworks attainable by the standard preparative methods. On the other hand, their potential use as photochromes or redox mediaters in coupled electron-transfer reactions provides an additional stimulus for future studies in this field.     

Assessment of density functional theory optimized basis sets for gradient corrected functionals to transition metal systems: the case of small Nin (n<or=5) clusters

Density functional calculations have been performed for small nickel clusters, Ni(n), Ni(n) (+), and Ni(n)(-) (n相似文献   

Structures of mixed gold-silver cluster cations (Ag(m)Au(n)+, m+n<6): ion mobility measurements and density-functional calculations

The collision cross sections of Ag(m)Au(n)+ (m+n)<6 cluster ions were determined. For bimetallic clusters, we observe a significant intracluster charge transfer leaving most of the ions positive charge on the silver atoms. The mixed trimeric ions Ag2Au+ and AgAu2+ are triangular like the pure gold and silver trimers. Most of the tetrameric clusters are rhombus shaped, with the exception of Ag3Au+, which has a Y structure with the gold atom in the center. Among the pentamers we find distorted X structures for all systems. For Ag2Au3+ we find an additional isomer which is a trigonal bipyramid. These findings are in line with predictions based on density-functional theory calculations, i.e., all these structures either represent the global minima or are within less than 0.1 eV of the predicted global minimum.     

Trends in structural, electronic and energetic properties of bimetallic vanadium-gold clusters Au(n)V with n = 1-14

A systematic quantum chemical investigation on the electronic, geometric and energetic properties of Au(n)V clusters with n = 1-14 in both neutral and anionic states is performed using BP86/cc-pVTZ-PP calculations. Most clusters having an even number of electrons prefer a high spin state. For odd-electron systems, a quartet state is consistently favoured as the ground state up to Au(8)V. The larger sized Au(10)V, Au(12)V and Au(14)V prefer a doublet state. The clusters prefer 2D geometries up to Au(8)V involving a weak charge transfer. The larger systems bear 3D conformations with a more effective electron transfer from Au to V. The lowest-energy structure of a size Au(n)V is built upon the most stable form of Au(n-1)V. During the growth, V is endohedrally doped in order to maximize its coordination numbers and augment the charge transfer. Energetic properties, including the binding energies, embedding energies and second-order energy differences, show that the presence of a V atom enhances considerably the thermodynamic stability of odd-numbered gold clusters but reduces that of even-numbered systems. The atomic shape has an apparently more important effect on the clusters stability than the electronic structure. Especially, if both atomic shape and electronic condition are satisfied, the resulting cluster becomes particularly stable such as the anion Au(12)V(-), which can thus combine with the cation Au(+) to form a superatomic molecule of the type [Au(12)V]Au. Numerous lower-lying electronic states of these clusters are very close in energy, in such a way that DFT computations cannot clearly establish their ground electronic states. Calculated results demonstrate the existence of structural isomers with comparable energy content for several species including Au(9)V, Au(10)V, Au(13)V and Au(14)V.     

Cucurbit[7]uril‐Dimethyllysine Recognition in a Model Protein

Here, we provide the first structural characterization of host–guest complexation between cucurbit[7]uril ( Q7 ) and dimethyllysine (KMe₂) in a model protein. Binding was dominated by complete encapsulation of the dimethylammonium functional group. While selectivity for the most sterically accessible dimethyllysine was observed both in solution and in the solid state, three different modes of Q7 ‐KMe₂ complexation were revealed by X‐ray crystallography. The crystal structures revealed also entrapped water molecules that solvated the ammonium group within the Q7 cavity. Remarkable Q7 ‐protein assemblies, including inter‐locked octahedral cages that comprise 24 protein trimers, occurred in the solid state. Cucurbituril clusters appear to be responsible for these assemblies, suggesting a strategy to generate controlled protein architectures.