Structural Characterizations

The various techniques available for structural characterization may be grouped under the following categories optical methods, diffraction methods, electron microscopic 

Magnetic resonance imaging (MRI) is a more recent but very powerful tool used for structural characterization, in particular the determination of the average pore size [194-197]. MRI provides direct visualization of a deliberately introduced pore gas inside the aerogel and thus offers information on its microscopic morphology. The average pore size is obtained from the estimated diffusion coefficients. 

The methods of structure determination of supported nanoclusters are essentially the same as those mentioned previously for supported metal complexes. EXAFS spectroscopy plays a more dominant role for the metal clusters than for the complexes because it provides good evidence of metal-metal bonds. Combined with density functional theory, EXAFS spectroscopy has provided much of the structural foundation for investigation of supported metal clusters. EXAFS spectroscopy provides accurate determinations of metal-metal distances ( 1-2%), but it gives only average structural information and relatively imprecise values of coordination numbers. EXAFS spectroscopy provides structure data that are most precise when the clusters are extremely small (containing about six or fewer atoms) and nearly uniform (Alexeev and Gates, 2000). 

The theoretical parameters characterizing Ir4 in zeolite NaX (Fig. 3) indicate Ir-O distances of about 2.2 A, in good agreement with EXAFS data (Ferrari et al., 1999) and approximately equal to the metal-oxygen bond distances found experimentally and theoretically for supported metal complexes, as discussed above. When the structure of Fig. 3 is rotated 60°, the theory indicates an Ir-O distance of about 2.7 A, in agreement with the longer distances observed by EXAFS spectroscopy (but this agreement may be fortuitous). 

The rates of toluene hydrogenation catalyzed by Ir4 and by Ir6 supported on metal oxides and zeolites differ from each other, typically by factors of 

EXAFS Results Characterizing Supported Metal Clusters During Catalytic Hydrogenation of Propene Fed in an Equimolar Mixture to a Flow Reactor Operated at Steady State at 25°C and 1 atm (Panjabi, Argo, and Gates, 1999)a 

The cluster-size dependence has not yet been explained it may reflect an intrinsically low activity of the clusters, but it might also be a consequence of increasing removal of residual ligands such as C from the clusters with increasing severity of treatment in H2. Other possibilities include a steric effect of the support, limiting adsorption of the reactants on the metal— such an effect would be greatest for the smallest clusters. Electronic effects should not be ruled out. 

Only a few compounds Ln(OR) (x = 2,3) studied with the X-ray diffraction method are monomeric in crystalline state. One of them, Yb(OQH3Ph2-2,6)3 [26] has been quoted already in Section IV.V. as a compound with a 7i-arene-lanthanoid bond. The structures of other compounds are given below. 

The structurally characterized complexes Ln(OR)3(B)2 containing two coordinative ligands have a different coordination at the Ln atom. In the molecule Ce[OC6H3-(t-Bu)2-2,6]3(t-BuNC)2 [23], which has a distorted trigonal-bipyramidal structure, one t-BuNC ligand occupies the axial position and the other one is in the equatorial plane. 

The complex Yb(OC6H3Ph2-2,6)3(THF)2 has a distorted square-pyramidal structure with two transoid aryloxide oxygens and two transoid THF oxygens in the basic plane [26]. They are planar within 0.01 A. The deviation of the Yb atom from this plane is 0.57 A towards the apical aryloxide oxygen atom. The Yb-O(aryloxide) and Yb-O(THF) distances are 2.038, 2.111, 2.048 A and 2.305, 2.305 A, respectively. 

The tert-butylcalix[8]arene derivative [Eu2(C88Hi06O8)(DMF)5](DMF)4 (DMF=dimethyl-formamide) is also dimeric with the central Eu2( X-0)2 fragment [52]. 

The titled compounds together with the compounds considered in the previous section form the general group of REM alkoxides. Their properties are listed in Table Vin.3. 

Chemical constitution, steric configuration, and, in some cases, details about chain conformation, aggregation, association, and supramolecular selforganization behavior of macromolecular substances can be determined using high-resolution nuclear magnetic resonance (NMR) spectroscopy. 

The limit of accuracy of H-NMR experiments carried out in dilute solution is around 1-5%, depending on the resolution of the spectrum, and of approximately 10% for C NMR. If the polymer to be investigated proved to be insoluble, solid-state NMR techniques are available for further investigation. Solid-state NMR methods are also very useful for determining bulk properties of polymers such as relaxation behavior of local motions and mutual arrangements of chains and chain segments. 

FIGURE 4.1 (a) Synthetic scheme of complex biohybrid structures composed of 

FIGURE 4.2 C NMR of structures B and C (Fig. 4.1) of maltose-modified hyper-branched PEI showing the influence of different degrees of maltose attachment on hyperbranched PEI scaffold (Fig. 4.1). Source Appelhans et al. [3]. Reproduced with permission of American Chemical Society. 

Using data pools and programs that simulate IR spectra, it is possible nowadays to characterize nearly all kinds of polymers very quickly using IR spectroscopy with respect to their constitution and their composition. Also, IR 

Most of the applications of electron diffraction intensities for structure analysis rely on a kinematical approximation and thus do not account for the effects of dynamical multiple diffraction. The use of intensities which may be strongly perturbed by multiple scattering results in many cases in poor or misleading structure indications in the direct methods results. One approach which can be shown to reduce dynamical effects somewhat is to use precession electron diffraction (RED) [67] which involves conical rotation of the incident beam about a zone axis direction and thus avoids the strongly dynamical direct zone axis orientation. Although the intensities collected with this technique are still significantly perturbed by dynamical effects [68, 69] results obtained by this approach for zeoHtes are encouraging [70-72]. 

In most (but certainly not all ) experiments involving ion-molecule reactions, the structure of the product ions is not determined. As the number of atoms in the product ions increases, the multiplicity of possible isomers becomes greater. Knowledge of the structure of ions is critical in determining what neutral products result from dissociative recombination. Although some classes of ion-molecule reactions, such as proton transfer reactions, lead to products with relatively well-characterized structures, the problem can be more severe with other classes of reactions. 

Consider, for example, the well-studied reaction between C+ and NH3, for which one set of products consists of the ion CH2N+ + H. But what is the structure of the product ion Based on detailed quantum chemical studies of the very complex potential surface, it is likely that two isomers are produced initially—the linear HCNH+ ion and the T-shaped H2NC+form89—although it is also possible that the latter form can subsequently isomerize via a unimolecular path into the more stable 

Association reactions, in particular, seem to present a severe problem for structural determination. In these reactions, an ion and a neutral species form a complex which is stabilized either by collision with a third body or, at especially low pressures, by the emission of radiation. The radiative mechanism, prominent in interstellar chemistry, is discussed below. Although some studies of radiative association have been performed in the laboratory,30,31 90 most association reactions studied are three-body in nature. It is customarily assumed that the product of three-body association is the same as that of radiative association, although this assumption need not be universally valid. 

A clearer case of a mistake being made by interstellar modelers concerns the association reaction, 

A recent study by Matthews et al.94 on the reactivity of products of the association reactions, 

For a long time (and also currently), drug discovery programs have typically used organic solvents such as methanol, butanol, ethyl acetate, chloroform, or hexane for 

Modem Alkaloids Structure, Isolation, Synthesis and Biology. Edited by E. Fattorusso and O. Taglialatela-Scafati Copyright 2008 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim ISBN 978-3-527-31521-5 

The 0-0 bond length in the O2 chemisorbed supported island ranges in fact from 1.29 A for a CosPt substrate to 1.33 A for Ni (see Table 3) its gas-phase value is 1.21 A. By way of comparison, for an O2 molecule adsorbed on a bridge-site on a Pt(lll) surface the experimental value of its bond length is in the range 1.37-1.39 A.  

Despite of the above differences, these results again show the similarity between mechanically alloyed and melt-spun samples. Maybe more interesting is to look for differing or advantageous properties of mechanically alloyed samples. Grutter [3.45] found that our mechanically alloyed Fe91Zr9, material 

Squares = experimental data solid line = calculated ratio for core-shell structure dotted line = calculated ratio for alloy formation. Reproduced from Ref [7]. 

High-resolution XPS provides quantitative evidence for shell growth based on the finite escape depth, X, of photoelectrons from the core atoms 26]. The typical escape depths are on the order of the shell thickness, and the photoelectron signal from core atoms should decrease accordingly in the core-shell structure [68]. 

To further prove the interpretation of the XRD data, and to obtain more quantitative information concerning the core-shell structures, the powder diffraction patterns were simulated [7, 69]. Nanocrystals were built by stacking planes along the (111) axis of the cubic lattice, and the sum of the specified core radius, r, and shell thickness, tj, was used to carve out the nanocrystal, assuming a spherical shape. 

For InAs-CdSe core-shells, the lattice mismatch was zero, and the experimental peak positions did not shift vdth shell grovrth (this was well reproduced in the simulation). An additional stacking fault was added in the shell region for the thicker shell of three monolayers, so as to better reproduce the experimental pattern. 

XRR of Fe/AI MLS (a) as-deposited (inset—thickness t versus scattered density profiie Rho) (b) anneaied at 623 K for 1 h (c) anneaied at 723 K for 4 h. (Reprinted with permission from Ref. 53. Copyright (2008) by the American Institute of Physics.) 

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In recent years, advances in experimental capabilities have fueled a great deal of activity in the study of the electrified solid-liquid interface. This has been the subject of a recent workshop and review article [145] discussing structural characterization, interfacial dynamics and electrode materials. The field of surface chemistry has also received significant attention due to many surface-sensitive means to interrogate the molecular processes occurring at the electrode surface. Reviews by Hubbard [146, 147] and others [148] detail the progress. In this and the following section, we present only a brief summary of selected aspects of this field. 

Time-of-flight mass spectrometers have been used as detectors in a wider variety of experiments tlian any other mass spectrometer. This is especially true of spectroscopic applications, many of which are discussed in this encyclopedia. Unlike the other instruments described in this chapter, the TOP mass spectrometer is usually used for one purpose, to acquire the mass spectrum of a compound. They caimot generally be used for the kinds of ion-molecule chemistry discussed in this chapter, or structural characterization experiments such as collision-induced dissociation. Plowever, they are easily used as detectors for spectroscopic applications such as multi-photoionization (for the spectroscopy of molecular excited states) [38], zero kinetic energy electron spectroscopy [39] (ZEKE, for the precise measurement of ionization energies) and comcidence measurements (such as photoelectron-photoion coincidence spectroscopy [40] for the measurement of ion fragmentation breakdown diagrams). 

Porter M D, Bright T B, Allara D L and Chidsey C E D 1987 Spontaneously organized molecular assemblies. 4. Structural characterization of normal-alkyl thiol monolayers on gold by optical ellipsometry, infrared-spectroscopy, and electrochemistry J. Am. Chem. Soc. 109 3559-68... 

Nuzzo R G, Dubois L FI and Allara D L 1990 Fundamental-studies of microscopic wetting on organic-surfaces. 1. formation and structural characterization of a self-consistent series of polyfunctional organic monolayers J. Am. Chem. Soc. 112 558-69... 

Bawendi M G ef a/1989 X-ray structural characterization of larger CdSe semiconductor clusters J. Chem. Phys. 91 7282... 

Fast and accurate predictions of H NMR chemical shifts of organic compounds arc of great intcrc.st for automatic stnicturc elucidation, for the analysi.s of combinatorial libraries, and, of course, for assisting experimental chemists in the structural characterization of small data sets of compounds. 

BW Beck, Q Xie, T Ichiye. Computational study of S—H S hydrogen bonds m [4Ee-4S]-type ferredoxm x-ray and NMR structures Characterization and implications for redox potentials. Protein Sci, submitted. 

Element-selective phase identification and quandfica-tion, structural characterization of disordered states... 

A,/2 for topography characterization much smaller for periodic structure characterization (A, is the laser wavelength used to illuminate the sample)... 

Raman spectroscopy is primarily a structural characterization tool. The spectrum is more sensitive to the lengths, streng ths, and arrangement of bonds in a material than it is to the chemical composition. The Raman spectmm of crystals likewise responds more to details of defects and disorder than to trace impurities and related chemical imperfections. 

Rodrigucz-Rcinoso, F., Activated carbon structure, characterization,... 

Radical cations can be derived from aromatic hydrocarbons or alkenes by one-electron oxidation. Antimony trichloride and pentachloride are among the chemical oxidants that have been used. Photodissociation or y-radiation can generate radical cations from aromatic hydrocarbons. Most radical cations derived from hydrocarbons have limited stability, but EPR spectral parameters have permitted structural characterization. The radical cations can be generated electrochemically, and some oxidation potentials are included in Table 12.1. The potentials correlate with the HOMO levels of the hydrocarbons. The higher the HOMO, the more easily oxidized is the hydrocarbon. 

High-resolution transmission electron microscopy (HREM) is the technique best suited for the structural characterization of nanometer-sized graphitic particles. In-situ processing of fullerene-related structures may be performed, and it has been shown that carbonaceous materials transform themselves into quasi-spherical onion-like graphitic particles under the effect of intense electron irradiation[l 1],... 

Pleated p sheet (Section 27.19) Type of protein secondary structure characterized by hydrogen bonds between NH and C=0 groups of adjacent parallel peptide chains. The individual chains are in an extended zigzag conformation. 

The thiotrithiazyl cation in [S4N3]C1 was one of the first S-N heterocycles to be prepared and structurally characterized. It is obtained as a reasonably air-stable, yellow solid by the reaction of S4N4 or [SsNaClJCl with S2CI2 in CCI4 (Eq. 5.12)." ... 

A variety of complexes of the thionyl imide anion [NSO] with both early and late transition-metal complexes have been prepared and structurally characterized. Since both ionic and covalent derivatives of this anion are readily prepared, e.g., K[NSO], McsMNSO (M = Si, Sn) or Hg(NSO)2, metathetical reactions of these reagents with transition-metal halide complexes represent the most general synthetic method for the preparation of these complexes (Eq. 7.10 and 7.11). ... 

MeNSO and 120° in HNSO, cf. 119° in SO2. The trityl derivative PhsCNSO is the only alkyl derivative to have been structurally characterized in the solid state. 

A number of transition-metal complexes of RNSO ligands have been structurally characterized. Three bonding modes, r(A,5), o-(5)-trigonal and o (5 )-pyramidal, have been observed (Scheme 9.1). Side-on (N,S) coordination is favoured by electron-rich (et or j °) metal centers, while the ff(S)-trigonal mode is preferred for less electron-rich metal centres (or those with competitive strong r-acid co-ligands). As expected ti (N,S)... 

There is no evidence for the tellurium analogues ArN=Te, but the cyclic trimers (EN Bu)3 (E = Se, Te) are stable crystalline solids that have been structurally characterized (Section 6.3). 

The only selenium diimide to be structurally characterized in the solid state, Se(NAd)2 (Ad = adamantyl), ° adopts the cis, trans conformation consistent with conclusions based on H and C NMR studies for Se(N Bu)2. ... 

The structure of the isomeric benzo-l,2,3-thiadiazole 11.30 is unknown, but the 1 1 adduct with AsFs (11.31) has been structurally characterized. The AsFs molecule is coordinated to the carbon-bonded nitrogen atom. Cycloocteno-l,2,3-selenadiazole is an effective source of selenium for the production of semi-conductors such as cadmium selenide." ... 

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