The substrate structure

Let us start with the simple case of an ideal crystal with one atom per unit cell that is cut along a plane, and assume that the surface does not change. The resulting surface structure can then be described by specifying the bulk crystal structure and the relative orientation of the cutting plane. This ideal surface structure is called the substrate structure. The orientation of the cutting plane and thus of the surface is commonly notated by use of the so-called Miller indices. 

Miller indices are determined in the following way1 (Fig. 8.1) The intersections of the cutting plane with the three crystal axes are expressed in units of the lattice constants. Then the inverse values of these three numbers are taken. This usually leads to non-integer numbers. All numbers are multiplied by the same multiplicator to obtain the smallest possible triple of integer numbers. The triple of these three numbers h, k, and l is written as (hkl) to indicate the orientation of this plane and all parallel planes. Negative numbers are written as n instead of —n. The notation hkl is used specify the hkl) planes and all symmetrical equivalent planes. In a cubic crystal, for example, the (100), (010), and (001) are all equivalent and summarized as 100.  

1 A more general definition of the Miller indices is given in the appendix on diffraction in the context of the reciprocal 

Hexagonal close packed crystals are often characterized using four lattice vectors. In this case four Miller indices (h k i l) are used correspondingly, where the fourth index is related to the first two indices by i = — (h + k). 

In surface science, often low-index surfaces, i.e. crystal surfaces with low Miller indices, are of special interest. In Fig. 8.2 the three most important low-index surfaces of a face centered cubic lattice are shown. The (100) is equivalent to the (010) and the (001) surfaces, the (110) is equivalent to the (Oil) and the (101) surfaces. 

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The ESDIAD pattern does, however, provide very usefril infomiation on the nature and synnnetry of an adsorbate. As an example, figure A1.7.13(a) shows the ESDIAD pattern of desorbed collected from a 0.25 ML coverage of PF on Ru(OOOl) [89]. The pattern displays a ring of emission, which indicates that the molecule adsorbs intact and is bonded tlirough the P end. It freely rotates about the P-Ru bond so that tlie emission occurs at all azimuthal angles, regardless of the substrate structure. In figure A1.7.13(b), the... 

For the preparation of 2,3-dihydroindoles (8) from indoles (7), two reduction methods are known. In the column Reduction Method in the table, the one indicated A represents use of EtsSiH in TFA (79JOC4809) and the other, indicated B, employs NaBHsCN in AcOH (77S859, 88JMC1746). Although both methods are applicable, the former is generally superior to the latter. In some cases, depending on the substrates structures, the reverse cases are also observed. Examples are the reactions marked B in the column. 

EH can be used in this case to obtain direct information on the substrate structure, and to characterize the growth process of metal catalysts. 

There are several ways to model the substrate. The simplest would be to consider the substrate as a structureless attractive wall. However, since we want the polymer molecules to be parallel to each other on the substrate, we impose a directional force. In 2D crystallization, we took the substrate structure into account by use of the continuous substrate potential t/2, a sort of mean field potential that restricts the molecular motion on the substrate [20] ... 

The question is When is it epitaxy Does the deposit have to have the same unit cell, or does it just have to be commensurate, in register with the substrate structure What size single crystal grains need to form to call it epitaxy Is it only nonepitaxial when the deposit is incommensurate with the substrate, or when it is amorphous ... 

The quality of an elemental deposit is a function of the deposition rate, surface diffusion, the exchange current and the substrate structure. Electrodeposition of a compound thin-film not only requires all these things, but stoichiometry as well. Under ideal conditions, the mass transfer rates and discharge rates of two elemental precursors can be tuned to produce a deposit with the correct overall stoichiometry for a compound. Whether the two elements will form the right compound, or a compound at all, is another question. 

In the system copper on Au(lll) [101, 102], the substrate structure controls nucleation despite the presence of a UPD layer. STM images obtained by Nichols et al. 

Otera and coworkers developed an alternative procedure to the Julia method for generating dienes or alkynes in the same reaction by the double elimination of /J-acetoxy or /1-alkoxy sulphones with potassium /-butoxide (equation 58)98,99. The reaction pathway leading to the diene or an alkyne depends on the substrate structure and the reaction conditions. If an allylic hydrogen is present in the substrate then diene is formed, otherwise, the alkyne is the product of the reaction. This modified Julia methodology has een applied to the synthesis of vitamin A (equation 59)100, alkaloids piperine (equation and trichonine (equation 61)102. 

The dimerization reaction has been applied to intramolecular cyclization of bis(diene)s, leading to the formation of five- and six-membered ring products bearing two allylic silane moieties (Equation (42)).125 Although stereoselectivity depends on the substrate structure, trans-(E,Z) isomers are generally favored in the five-membered ring formations. 

Intramolecular coupling Some aromatic diketones have been stereoselectively cy-clized under various electrolysis conditions, which, together with the substrate structure, strongly influence the stereochemistry of the formed cyclic diol. Reductive cyclization of 1,8-diaroylnaphthalenes led to trans-diols, 2,2 -diaroylbiphenyls and a, )-diaroylalkanes yielded cis-diols with different stereoselectivities depending on substrate structure and electrolysis conditions (pH, cosolvent) (Fig. 57) [310-312]. 

A concise description of the requirements concerning the substrate structure, nature of the introducing group, and reaction medium is discussed in the following text. 

As discussed above, accumulated data demonstrate that the catalyst, the substrate structure, and other competing metallocarbene pathways significantly affect the ylide formation and the subsequent rearrangement process. West and co-workers have recently studied selectivity in rearrangement via five- or six-membered oxonium ylides by... 

In several cases where epitaxial growth occurs involving the ion-by-ion mechanism, the crystal structure is dictated by the substrate structure. This is treated separately in Section 4.1.5. 

The bio-oxidants that are formed are highly suited to attacking organic molecules by attracting the most readily available electrons in the substrates structures (Table 17.4). Often these are -electrons of aromatic rings and carbon-carbon double bonds ... 

The general preference of 1,3-anti relationship induced by the substrate structure may be understood by assuming that the transition states me those shown in Scheme 58. The preference for the anti transition feructure originates primarily from the (7 )-BINAP chirality (Scheme 51). addition, the six-membered ring in the syn-generating transition ucture suffers l,3-R2/0 repulsion, which is absent in the diastereo-iric anti transition state. 

The hydrogen bond between the N-acylamino NH and the carbonyl of Ser-214 initiates a short region of antiparallel /3 sheet between the residues Ser-214, Trp-215, and Gly-216 of the enzyme and the amino acids P], P2, and P3 of the substrate (structure 1.9). 

It was pointed out over 60 years ago that the recognition of a chiral (or, as subsequently realized, a prochiral) carbon by an enzyme implies that at least three of the groups surrounding the carbon atom must interact with the enzyme. This is the multi-point attachment theory.4 If only two of the groups interact, the other two may be interchanged without affecting the binding of the substrate (structures 8.9). 

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