Structure equivalence

To answer the first question, Lesk and Chothia examined in detail residues at structurally equivalent positions that are involved in helix-heme contacts and in packing the a helices against each other. After comparing the nine globin structures then known, the 59 positions they found that fulfilled these criteria were divided into 31 positions buried in the interior of the protein and 28 in contact with the heme group. These positions are the principal determinants of both the function and the three-dimensional structure of the globin family. 

Tom Blundell has answered these questions by superposing the Ca atoms of the two motifs within a domain with each other and by superposing the Ca atoms of the two domains with each other. As a rule of thumb, when two structures superpose with a mean deviation of less than 2 A they are considered structurally equivalent. For each pair of motifs Blundell found that 40 Ca atoms superpose with a mean distance of 1.4 A. These 40 Ca atoms within each motif are therefore structurally equivalent. Since each motif comprises only 43 or 44 amino acid residues in total, these comparisons show that the structures of the complete motifs are very similar. Not only are the individual motifs similar in stmcture, but they are also pairwise arranged into the two domains in a similar way since superposition of the two domains showed that about 80 Ca atoms of each domain were structurally equivalent. 

From all of this, we can deduce that this transition structure connects two structurally-equivalent minima, and that the path between them corresponds to J methyl rotation. This is not a very interesting transition structure. 

Structural Equivalence of Watson-Crick Base Pairs... 

The group A may be regarded as a structural equivalent for the carbonyl group B, since introduction of A into a molecule is actually an indirect means of introducing B. It is convenient to have a word for units within molecules such a word is synthon, introduced by Corey, which is defined as a structural unit within a molecule that can be formed and/or assembled by known or conceivable synthetic operations. There are many other synthons equivalent to A and B, for example, C (by Reactions 16-23 and 19-3) and D (by Reactions 10-2 and 16-22). ... 

Conformationally restricted analogs of substrates can be useful in elucidating both the substrate specificities and the product specificities of enzymes. The restriction can help stabilize an intermediate in the enzymatic process so that it may be isolated. Two or more otherwise structurally equivalent portions of a substrate may be rendered nonequivalent by the restriction so that potential differentiation of these portions by the enzyme in determining product specificity may be investigated. 

While structurally equivalent, they usually differ from a reactivity point of view. Firstly, the organometallic reagent, after reaction with the surface, readily extrudes extra ligands upon reaction with surface silanols, while they can give a stable adduct in solution. 

The main structural difference between trigonal- and tetragonal-prismatic clusters [12,77] is that not all technetium atoms of the latter are structurally equivalent a pair of technetium atoms situated on the long diagonal of the rhombic base in tetragonal-prismatic clusters have the 2.0 + formal oxidation state, whereas the technetium atoms situated on the short diagonal of these rhombs have the formal oxidation state 1.0 +. However, X-ray photoelectron... 

Rohmer, M., P. Bouvier, and G. Ourisson. 1979. Molecular evolution of biomembranes structural equivalents and phylogenetic precursors of sterols. Proc. Natl. Acad. Sci. USA 76 847-851. 

The general formula of these new oxynitrides M2M1(PX3)3 suggests as for the previous series a cyclophosphate-type structure or a long-chain polyphosphate-type structure, where nitrogen would be structurally equivalent to oxygen. 

Methyl deoxypodocarpate 127 (Scheme 1) 129) represents a simple problem since the ketone 132 is well-known and readily available from Hagemann s ester in three steps. The problem of geminal alkylation of this ketone stems from its existence as an EjZ mixture of ring fusion isomers. Recognizing that decarbonylation of aldehydes occurs readily with Wilkinson s catalyst creates a structural equivalence of an acetaldehyde chain and a methyl group as in 128. This simple relationship immediately establishes several options, a simple one uses a thioacetal such as 129 as a synthon for the aldehyde. The presence of a carbonyl group three carbons away... 

X-Ray photoelectric ionization is believed to take place in a time interval of about 10-18 s. Therefore separate XPS peaks are possible for atoms if the lifetime of the asymmetric electronic state is greater than about 10 18 s, whether or not the atoms are structurally equivalent. We may represent the ground state of a localized mixed valence compound (involving two metal atoms differing in oxidation state by one unit) by the following formula, where the dot represents the extra valence electron M—M. The two possible XPS transitions can then be represented as follows, where the asterisk indicates core ionization,... 

Representation of the Molecule in LISP. We have used the chemist s sketch, or its Lewis structure equivalent, as the model of a data structure in LISP ( ). This language has the flexibility needed to express an essentially non-numerical object, in terms of lists. LISP will permit us to organize molecular structure information in a way that mimics the human expert s knowledge. To accomplish this representation, we must develop a clear idea how the chemist assimilates the information provided directly and explicitly by the sketch, and how the properties of the molecule are recalled to the chemist s awareness. 

The free energy yisid of these reactions has been estimated by assuming the organic matter is structurally equivalent to glucose with respect to the carbon, a primary amine with respect to the nitrogen, and glucose-1 -phosphate with respect to phosphorus. Multplication by 17.67 will convert these values to kilojoule per Redfield-molecule mole. 

A further interesting X-ray structural study has been that of (AsPh4)2-[Pd2(N3)6] (66). This reveals similar asymmetry in the two N—N bond lengths for the bridging (1.239 and 1.142 A) and terminal (1.205 and 1.139 A) azide groups. Such structural equivalence indicates that there is no appreciable change in electronic character when a terminal azide co-ordinates to a second Pd via a normally unshared electron pair on the trigonal N atom (see Table... 

The adenine radical cation was observed in a single crystal of adenine hydrochloride hemihydrate [43]. In this crystal, the adenine is protonated at Nl. After electron loss, the molecule deprotonates at Nl, giving Ade(Nl -l-H, Nl-H). This produces a radical that is structurally equivalent to the cation of the neutral adenine molecule with spin density on C8 and N6 [p(C8) = 0.17 and p(N6) = 0.25]. The adenine radical cation is strongly acidic (pi a< 1) [22]. This strong driving force makes the reaction independent of environmental conditions. In single crystals of adenosine [42] and anhydrous deoxyadenosine [44], the N6 deprotonated cation [Ade(N6-H) ] is observed which is characterized by p(C8) = 0.16 and p(N6) = 0.42. The experimental isotropic hyperfine couplings are N6-H = 33.9 MHz and C8-H = 12.4 MHz. 

Despite the structural equivalence of the twelve metal centers in the o -PWi204o Keggin anion, a stepwise reduction of the tungsten centers is observed [30f]. EPR experiments on this species show that the added electron is delocalized (type II in the scheme proposed hy Rohin and Day) [4]. Over all 12 tungsten centers suggesting that there is communication... 

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