CTP scheme

Although relatively small, the experience of the comparative computations available from the literature generally agrees with this conclusion. In this respect the MINDO/3 realization of the CTP scheme (13) is quite representative. Although, as in the case of CNDO/BW, the hydrogen Is AO was chosen for Xa> the exponent of the STO was adopted to be (as for the sp3 AO of Si)... 

Let us return to the results obtained in the CNDO/BW realization of the CTP scheme. The calculations for the Si(OA)4 cluster la give a quasi-band picture of electron levels with HOMO-LUMO splitting of 12eV that is somewhat (but quite reasonably) higher than the experimental estimate of the band gap in Si02. The HOMO is mainly composed of 2p AOs of O atoms, whereas the LUMO is constituted by 3s AOs of Si that are quite in agreement with the band structure of Si02. 

Fig. 1. (a) Extended and (b) minimal clusters used in choosing the parameters for pseudoaluminum in the CTP scheme. The atomic charges are presented in the figure. 

Cluster Modeling of Terminal Hydroxyl Groups of Different Acidities [(AO)3S OH Cluster, CTP Scheme, CNDO/BW Method]... 

Close conclusions were also drawn in our studies using the CTP scheme and CNDO/BW method. Extensive variation of the acid-base properties of a terminal OH group by means of systematic change of VOIPA from 7 to 16 eV in the HOSi(OA)3 cluster (Table I) did not noticeably affect the shape of the potential curve of the OH bond (Fig. 2). However, in the presence of an adsorbed ethylene molecule, the curve deviated considerably (48). This is in accordance with the known relatively slight differences in vOH for hydroxyl groups of different acidity and the pronounced effect of the acidity on the shift, Avoh, caused by adsorption of some molecules (51). 

Senchenya et al. (96) have treated the adsorption of ethanol on a structural hydroxyl group (Fig. 14) using a CTP scheme and the CNDO/BW method. The separation of a molecule and cluster with respect to the z axis was optimized, the optimal values being r = 1.19 A and R = 1.28 A The adsorption energy was 23.2 kcal/mol, which was close to the experimental value (97). Note that this was essentially the two-point adsorption involving both acid and base sites. This case is quite similar to the above propylene adsorption (90). There is also no definite trend toward proton transfer from the hydroxyl group of a zeolite to the alcohol molecule. The carbocation state is also predicted to be activated. This, in turn, increases relative efficiency of the synchronous mechanism (with the same recommendation for its experimental examination). The estimation (96) of the energetics of the intermediate structures of the synchronous mechanism showed that such a mechanism is quite realistic. 

There are three traditional structures usually adopted as probable BASs in amorphous aluminosilicates a water molecule coordinated by an electron-acceptor center (I), a bridged OH group (II), and a surface H30 + ion (III) (125,126). The catalytic activity of these sites is obviously determined by their properties and surface concentrations. Pelmenshchikov et al. (127) have attempted to compare these characteristics for the above types of BAS in aluminosilicates in terms of the cluster approach. For this purpose they considered a sequence of states of the model fragment of a dehydroxylated surface plus two water molecules (Fig. 15). State S0 corresponds to a dehydroxylated surface, states S, Sn, and Sm represent the sites of the I, II, and III types and states Sla and SIla correspond to centers I and II at a higher coverage. The relative energies of these structures obtained using the CTP scheme and the CNDO/BW technique are presented in Fig. 15. The relative surface density of the sites, og(nJnf), was estimated as the relative probability of their occurrence ... 

CMP-NeuAc synthetase (EC 2.7.7.43) to produce CMP-NeuAc. The by-product pyrophosphate (PPi) is hydrolyzed to phosphate (Pi) by inorganic pyrophosphatase (PPase). Sialyla-tion is accomplished with a2,3-sialyltransferase (< 2,3NeuAcT) or a2,6-sialyltransferase (a2,3NeuAcT), respectively. The released CMP is again converted to CDP, to CTP, and finally to CMP-NeuAc. The UDP-Gal and CMP-NeuAc regeneration schemes have been combined in a one-pot reaction and applied to the synthesis of sialyl Lewis X. 

Dolichyl phosphate phosphatase has been described in animal tissues,74-76 and it is possibly responsible for the free dolichol found in tissues. This free dolichol can be rephosphorylated by a dolichol kinase using cytidine triphosphate (CTP) as phosphoric donor,77-78 or acylated by a dolichol acyltransferase79 (see Scheme 1). 

Figure 4.3 Incorporation of PyC to position 75 in a tRNA transcript by CCA enzyme. (A) Chemical structure of PyCTP, where inward and outward arrows denote hydrogen bond acceptors and donors, respectively. (B) A scheme showing the cloverleaf of a tRNA-C74 transcript as the substrate for CCA addition, using PyCTP and ATP as the nucleotide donors. (C) Denaturing gel analysis (12% PAGE/7 M urea) of extension of the tRNA-C74 transcript by CCA enzyme, showing the tRNA transcript in lane 1, lack of extension of the transcript without CTP or PyCTP in lane 2, extension with polyC in lane 3, extension with C75—A76 in lane 4, extension with polyPyC in lane 5, and extension with PyC75-A76 in lane 6 (Zhang et al., 2008a).

In both schemes, the upper pathway represents the formation of an unstable intermediate that is then trapped by reaction with ATP. By contrast, the lower pathways represent activation of a carbonyl group by ATP, followed by loss of a proton (to form enol pyruvate eq. 9) or reaction with ammonia (to yield an intermediate for the formation of CTP eq. 10). ATP has long been known to drive metabolic processes if it phosphorylates carbonyl groups, it will prove to serve a catalytic role as well. 

Mikheikin et al. (11) have formulated an alternative approach where terminal valencies are saturated by monovalent atoms whose quantum-chemical parameters (the shape of AO, electronegativity, etc.) are specially adjusted for the better reproduction of given characteristics of the electron structure of the solid (the stoichiometry of the charge distribution, the band gap, the valence band structure, some experimental properties of the surface groups, etc.). Such atoms were termed pseudo-atoms and the procedure itself was called the method of a cluster with terminal pseudo-atoms (CTP). The corresponding scheme of quantum-chemical calculations was realized within the frames of CNDO/BW (77), MINDO/3 (13), and CNDO/2 (30) as well as within the scope of the nonempirical approach (16). 

It is worth noting that the above CTP computational scheme opens a simple and convenient way for computer simulation of qualitative dependences. Thus, systematic variation of VOIPA in the HOSi(OA)3 cluster results in the successive change of the acidity of OH groups (as represented by h+), and thereby the qualitative influence of the acidity of OH group on its chemisorption properties and reactivity with respect to a particular reaction can easily be followed. Such an approach was rather widely used in our works (35, 36). 

From the pyrrolinium-furanium ion equilibrium (Scheme 62) one can assume, in agreement with CTp values (—1.7 and —0.86 for 2-pyrrolyl and 2-furyl, respectively), that the pyrrole ring stabilizes the adjacent furanium cation better than vice versa. Thus, the selective pyrrole ring protonation at low temperature (—80 C) is most likely a kinetic result leading to the thermodynamically nonequilibrium state with the predominance of pyrrolium ions. 

To probe the transition state structure for these reactions further, the effect of para substituents on amide rotation rates was measured for a series of N,Af-dimethylbenzamides (Berarek, 1973). When the data are correlated with cTp (Ritchie and Sager, 1964), a p value of —1.14 0.06 is obtained (see Fig. 2). The negative p value indicates that electron-donating substituents accelerate the reaction. This can rationalized in the context of Scheme III, where resonance forms for these substrates are shown. The rotational barrier about the C—N bond is decreased as resonance forms I and III predominate. If R is electron donating, these resonance forms will contribute more to the structure of the amide than will II and C-N rotation will therefore be accelerated. 

Figure 3. Reaction scheme of complementary replication of single-stranded RNA. Reaction consists of four phases initiation, elongation, product release, and template reactivation. Reaction product (replica) is complementary to template. Substrates are four nucleoside triphosphates ATP, GTP, UTP, and CTP. Pyrophosphate (pp) is waste product at each step of incorporation. Symbols /, RNA template chain E, enzyme (replicase) P, growing RNA replica chain. Indexes A, association D, dissociaton S, substrate F, phosphate diester bond formation PR, product release the numbers 3, or 5, refer to end of the RNA chain to which the enzyme binds or from which it dissociates (cf. ref. 10).

Scheme L Synthesis of a2,64inked sialyl-N-acetyllactosamine using a one-pot multi-enzyme system with in situ regeneration of CMP-Neu5Ac. Abbreviations for enzymes CSS, CMP-sialic acid synthetase NMK, nucleoside monophosphate kinase PK, pyruvate kinase PPase, pyrophosphatase. Abbreviations for compounds PEP, phosphoenolpyruvate ADP, adenosine 5 -diphosphate ATP, adenosine 5 -triphosphate CMP, cytidine 5-monophosphate CDP, cytidine 5 -diphosphate CTP, cytidine 5-triphosphate LacNAc, N-acetyllactosamine NeuSAc, N-acetylneuraminic acid PPi, inorganic pyrophosphate.

Scheme 22 The whole biosynthetic pathway of sugar nucleotides. ATP, adenosine triphosphate Gal-1 -P, galactose-1-phosphate UTP, uridine triphosphate UDP, uridine diphosphate NAD, nicotinamide adenine dinucleotide Fru, fructose AcCoA, acetyl coenzyme-A PEP, phosphoenolpyruvate CTP, cytidine triphosphate NADP, nicotinamide adenine dinucieotide phosphate GTP, guanosine triphosphate.

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