Hydrogen-bond formation mechanism

Three mechanisms have been proposed to explain this behavior, namely (a) the TT-TT-dispersion interaction mechanism, (b) the hydrogen-bond formation mechanism and (c) the electron-donor-acceptor complex mechanism. To give these ideas a historical... 

A significant modification in the stereochemistry is observed when the double bond is conjugated with a group that can stabilize a carbocation intermediate. Most of the specific cases involve an aryl substituent. Examples of alkenes that give primarily syn addition are Z- and -l-phenylpropene, Z- and - -<-butylstyrene, l-phenyl-4-/-butylcyclohex-ene, and indene. The mechanism proposed for these additions features an ion pair as the key intermediate. Because of the greater stability of the carbocations in these molecules, concerted attack by halide ion is not required for complete carbon-hydrogen bond formation. If the ion pair formed by alkene protonation collapses to product faster than reorientation takes place, the result will be syn addition, since the proton and halide ion are initially on the same side of the molecule. 

The mechanism of the C02 transfer reaction with acetyl CoA to give mal-onyl CoA is thought to involve C02 as the reactive species. One proposal is that loss of C02 is favored by hydrogen-bond formation between the A -carboxy-biotin carbonyl group and a nearby acidic site in the enzyme. Simultaneous deprotonation of acetyl CoA by a basic site in the enzyme gives a thioester eno-late ion that can react with C02 as it is formed (Figure 29.6). 

Using molecular mechanics calculations to assess the three-dimensional shape of a molecule, various surface properties such as polarity and size can be calculated. The dynamic molecular surface properties can be determined from the (low energy) conformation(s) of the drug molecule obtained by molecular mechanics calculations of conformational preferences. The potential advantage of this method is that the calculated surface character-sitics determine numerous physicochemical properties of the molecules including lipophilicity, the energy of hydration and the hydrogen bond formation capacity [187-... 

Weiss, A. Hydrogen Bond Formation ofFormamide and N-Methylformamide in aqueous solution, studied by Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) University of Innsbruck Innsbruck, 2010. 

The activation parameters for the ethylenediamine complexes of rhodium(III) and iridium(III) are also in keeping with an essentially dissociative mechanism. The observation that AHt(k-t) is larger than AHt(k 2) for iridium(III) has been rationalized in terms of stabilization of the aquahydroxo species by intramolecular hydrogen bond formation. Similarly, the observation for the rhodium(III) system that AHl(k ) < AHt(k-2) for ammonia, whereas A// (, ) AHt(k 2) for ethylenediamine may, in part, by rationalized in terms of the observed differences in the degree of intramolecular hydrogen bond stabilization of the aqua hydroxo species in the two systems [ZCH(en) > J h(NH3) see Table XXI]. 

A mild, acid- and metal-free direct reductive amination of ketones has been achieved that relies on selective imine activation by hydrogen bond formation and utilizes the Hantzsch ester for transfer hydrogenation and catalytic amounts of thiourea as hydrogen bond donor. The mechanism in Scheme 18, supported by ab initio calculations, has been suggested.358... 

Of the same importance is another component of the mechanism—the display of acid-base properties of His 552 fragment. According to X-ray patterns, among two probable mechanisms of distal histidine interaction with hydrogen bond formation ... 

The use of chiral stationary phases (CSP) is a technique that relies on the formation of transient, temporary diastereoisomers between the sample enantiomers and the chiral stationary phase.1 Differences in stability between the diastereoisomers are reflected in differences in retention times the enantiomer that forms the least stable complex is eluted first. Chiral stationary phases may be classified into five different groups on the basis of mechanism of retention 77 (1) chiral phases with cavities78 80 (inclusion mechanism), shown in Figure 2.19, (2) chiral affinity phases,81,82 (3) chiral phases based on multiple hydrogen bond formation,83 (4) chiral jr-donor and... 

The mechanism of retention on chiral phases that is based on multiple hydrogen bonding formation involves the formation of base pairs and triple hydrogen bonds between the solutes and the chiral stationary phase 95 Fundamental work in this area has been done by Hara and Dobashi,96 97 using amino acid amide and tartaric acid amide phases. In addition, N,N -2,6-pyridinediyl bis(alkanamides) chemically bonded to silica gel have been described for the resolution of barbiturates 95... 

Two short pathways that link the a-helical and /3-hairpin macrostates without making use of microstates with an instantaneous temperature above 488K are shown in Fig.5.1. The path shown in Fig.5.1 (upper) involves the unwinding of both ends of the helix, leaving approximately one turn of helix in the middle of the molecule. This turn then serves as a nucleation point for the formation of the /3-turn, which is stabilized by hydrophobic interactions between the side chains of Y45 and F52. The native hydrogen bonds nearest to the turn then form, after which the remainder of the native hairpin structure forms. This pathway is similar to previously proposed mechanisms for the folding of the G-peptide /3-hairpin from a coil state, which emphasize the formation of hydrophobic contacts before hydrogen bond formation [17,18, 140-143] and the persistence of the /3-turn even in the unfolded state [143]. 

In addition, basic quantum mechanical calculations have shown that the change in isotropic H chemical shift (SH) due to hydrogen bond formation can be attributed primarily to O-H bond polarisation [80]. Similarly, the change in 2H quadrupole coupling constant is also expected to be caused by O-H bond polarisation. It would therefore be interesting to explore correlations between SH and the O-H bond length (r0 H) and correlations between e2qQlhand r0 H> as r0. H... 

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