Energetic favorability

D P f Goodford 1985. A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules. Journal of Medicinal Chemistry 28 849-857. Molecular Discovery Ltd, Oxford, United Kingdom. 

Configuration correlation diagram for homonuclear case in which homolytic bond cleavage is energetically favored. 

State correlation diagram for heteronuclear case in which both heterolytic bond cleavage products are energetically favored relative to homolytic cleavage. 

What happens when isomerization is performed is that the double bond of the allylbenzene safrole migrates to the more energetically favorable position between the alpha and beta carbons of the propyl side chain. Thus isosafrole, a propenylbenzene, is born. 

The N-basicity of the commonly used amines (pyrrolidine > piperidine > morpholine) drops by 2-3 orders of magnitude as a consequence of electron pair delocalization in the corresponding enamines. This effect is most pronounced in morpholino enamines (see table below). Furthermore there is a tendency of the five-membered ring to form an energetically favorable exocyclic double bond. This causes a much higher reactivity of pyrroUdino enamines as compared to the piperidino analogues towards electrophiles (G.A. Cook, 1969). 

Why do carbocations rearrange The answer is straightforward once we recall that tertiary carbocations are more stable than secondary carbocations (Section 4 10) Thus rearrangement of a secondary to a tertiary carbocation is energetically favorable As... 

Disubstituted cyclohexanes can exist as cis-trans isomers as well as axiaEequatorial conformers. Two isomers are predicted for 1,4-dimethylcyclohexane (see Fig. 1.9). For the trans isomer the diequatorial conformer is the energetically favorable form. Only one cis isomer is observed, since the two conformers of the cis compound are identical. Interconversion takes place between the conformational (equatoriaEaxial) isomers but not configurational (cis-trans) isomers. 

Two pathways were found for the chiral hydrogenation, and they give products with different stereochemistries (19). One pathway involves the preferred mode of initial binding of the reactant to the catalyst. The other pathway involves an isomer of the reactant—catalyst complex that is formed in only small amounts, but its conversion is energetically favorable and constitutes the kinetically predominant pathway to products (9) (Fig. 4). Thus the chirahty of the product is determined not by the preferred mode of the initial binding, but instead by the more favorable energetics of the pathway involving the minor isomer of the reactant—catalyst complex. 

PI Goodford. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. I Med Chem 28 849-957, 1985. 

Certain side-chain conformations are energetically favorable... 

Variations on the a helix in which the chain is either more loosely or more tightly coiled, with hydrogen bonds to residues n + 5 or n + 3 instead of n + 4 are called the n helix and 3io helix, respectively. The 3io helix has 3 residues per turn and contains 10 atoms between the hydrogen bond donor and acceptor, hence its name. Both the n helix and the 3to helix occur rarely and usually only at the ends of a helices or as single-turn helices. They are not energetically favorable, since the backbone atoms are too tightly packed in the 3io helix and so loosely packed in the n helix that there is a hole through the middle. Only in the a helix are the backbone atoms properly packed to provide a stable structure. 

In the lowest optieally excited state of the molecule, we have one eleetron (ti ) and one hole (/i ), each with spin 1/2 which couple through the Coulomb interaetion and can either form a singlet 5 state (5 = 0), or a triplet T state (S = 1). Since the electric dipole matrix element for optical transitions — ep A)/(me) does not depend on spin, there is a strong spin seleetion rule (AS = 0) for optical electric dipole transitions. This strong spin seleetion rule arises from the very weak spin-orbit interaction for carbon. Thus, to turn on electric dipole transitions, appropriate odd-parity vibrational modes must be admixed with the initial and (or) final electronic states, so that the w eak absorption below 2.5 eV involves optical transitions between appropriate vibronic levels. These vibronic levels are energetically favored by virtue... 

The principle of microscopic reversibility requires that the reverse process, ring closure of a butadiene to a cyclobutene, must also be a coiuotatory process. Usually, this is thermodynamically unfavorable, but a case in which the ring closure is energetically favorable is conversion of tra s,cis-2,4-cyclooctadiene (1) to bicyclo[4.2.0]oct-7-ene (2). The ring closure is favorable in this case because of the strain associated with the trans double bond. The ring closure occurs by a coiuotatory process. 

Bromination of methane is exothermic, but less exothermic than chlorination. The value calculated from bond dissociation energies is AH° = -30 kJ. Although bromination of methane is energetically favorable, economic considerations cause most of the methyl bromide prepared commercially to be made from methanol by reaction with hydrogen bromide. 

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