Skeleton coordinates, hydrogen atom

Quantum-chemical calculations of PES for carbonic acid dimers [Meier et al. 1982] have shown that at fixed heavy-atom coordinates the barrier is higher than 30kcal/mol, and distance between O atoms is 2.61-2.71 A. Stretching skeleton vibrations reduce this distance in the transition state to 2.45-2.35 A, when the barrier height becomes less than 3 kcal/mol. Meier et al. [1982] have stressed that the transfer is possible only due to the skeleton deformation, which shortens the distances for the hydrogen atom tunneling from 0.6-0.7 A to 0.3 A. The effective tunneling mass exceeds 2mn-... 

Whereas edge- and face-bridging hydrogen atoms are associated mainly with metal-metal orbitals already present in the tetrahedral skeleton (see last section) and therefore have limited steric requirements, terminal hydrides occupy a full coordination position. It is not surprising then that the only examples of tetrahedral species with terminal hydrides contain 11 and 10 carbonyls, [Ir4(CO)nH] and [Ir4(CO)ioH2]2 . (The assignment for [Ir4(CO)nH] is based on the structure determination of the analogous [Ir4(CO)nBr] and on the similarity of the ir spectra of the two species (11).)... 

Similar to SMILES, InChI does not store atom coordinates. In contrast to SMILES, which by default omits hydrogen atoms that are then added implicitly to match the most common valency of an atom, InChI stores hydrogen atoms but does not store bond orders. These two techniques are just different approaches to the same problem for a given molecular skeleton, the bond orders and number of hydrogen atoms... 

Having the three-dimensional coordinates of atoms in the molecules, we can convert these into Cartesian RDF descriptors of 128 components (B = 100 A ). To simplify the descriptor we can exclude hydrogen atoms, which do not essentially contribute to the skeleton structure. Finally, a wavelet transform can be applied using a Daubechies wavelet with 20 filter coefficients (D20) to compress the descriptor. A low-pass filter on resolution level 1 results in vectors containing 64 components. These descriptors can be encoded in binary format to allow fast comparison during descriptor search. 

Two sorts of reaction products can be distinguished. In the first case (Table 27.1a), the compounds are structurally very similar to the starting material (Ph2Si0)g[Al(0)0H]4, with the exception that the hydrogen atoms are replaced by metallic elements. In the second case (Table 27.1b), the skeleton is considerably modified, creating oxygen coordination holes which are occupied by the cations such as Li and K. Of the structures assembled in Table 27.1, two are depicted in more detail (Figure 27.4). The structure of the inner... 

Crystalline methyllithium consists of tetrameric aggregates (Fig. 3.4). Each carbon atom is bound to three hydrogen atoms and is equidistant from the three lithium atoms which are at the corners of a triangular face of the Li4 tetrahedron. The formal coordination number of carbon is therefore seven. The structure consists of two interpenetrating and unequal tetrahedra, one Li and one C. The Li C skeleton can thus be represented as a distorted cube. The methyl carbon of one tetramer is only 2.36 A from a lithium atom of a neighbouring tetramer. This interaction makes methyllithium involatile and sparingly soluble in hydrocarbons. v... 

Fig. 2 (Left) Two-dimensional brickwall motif in crystalline If via N-Li coordination. Right) Layer-by-layer stacked network in crystalline If. Hydrogen atoms, butyls, butadiene skeletons, and methyls on TMEDAs are omitted for clarity. C gray, N blue, Li dark red...

The X-ray crystal structure of [Pv TPP(OH)2 ]OH 2H2 O has been determined.32 The porphyrin skeleton is distorted S4 symmetrically to attain short P—distance ( 1.90 A). The hydroxy groups are strongly intermolecularly hydrogen bonded, and the phosphorus atom is displaced from the N4 plane by 0.096 A. The antimony(V) ion is centred in the porphyrin plane in [Sb(OEP)(OH)2]+ with a somewhat large Sb—distance of 2.065(6) A.31 The structure of [Bi(OEP)]NO, is of interest, since the four-coordinate BiUI ion protrudes from the porphyrin N4 plane by 1.09 A with a very long Bi—Npor distance of 2.32 A.31... 

Under similar procedure, di-Uthio compounds Ib-d (Type II, Scheme 2) could be obtained in high yield as a dimer in the solid state [30-32]. The aggregation states and coordination environment of Li atom depend on the substitution pattern and steric hindrance on butadiene skeleton. In the crystal stracture of la and lb, no external ligand is coordinated to Li atom, while in the crystal structure of Ic, THF ligands are only coordinated to the less-hindered, a-phenyl-substituted Li atom. In the crystal structure of Id, each Li atom is coordinated by one THF ligand. We suggest that Li atom in Id is much less hindered and easier to accept THF coordination because of only hydrogens on 1,4-position of butadiene skeleton [32]. 

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