Oxyanion Holes and Their Mimics

Pihko, Petri M.; Rapakko, Sanna; Wierenga, Rik K.

doi:10.1002/9783527627844.ch4

Cited by 31 publications

(37 citation statements)

References 103 publications

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“…[2] In both cases,acharge builds up on the carbonyl oxygen atom on the wayt oanegatively charged intermediate, such as at etrahedral intermediate or an enolate ion. [2] In the realm of small-molecule catalysis, hydrogen-bond donors, such as (thio)urea and squaramide functionalities, could be viewed as analogues of the oxyanion holes. [3] These functionalities are relatively rigid and flatt wo-point hydrogenbond donors.…”

Section: Introductionmentioning

confidence: 99%

“…[1,2] Oxyanion holes stabilize high-energyi ntermediates andt ransition states that bear negatively charged oxygen atoms in enzymatic reactions that involve tetrahedral intermediates (e.g.,h ydrolytic cleavage reactions of (thio)esters and amides) and reactions that involve enolatei ntermediates. [2] In both cases,acharge builds up on the carbonyl oxygen atom on the wayt oanegatively charged intermediate, such as at etrahedral intermediate or an enolate ion. [2] In the realm of small-molecule catalysis, hydrogen-bond donors, such as (thio)urea and squaramide functionalities, could be viewed as analogues of the oxyanion holes.…”

Section: Introductionmentioning

confidence: 99%

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Folding Patterns in a Family of Oligoamide Foldamers

Kortelainen

Suhonen

Hamza

et al. 2015

Chemistry A European J

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A series of small, unsymmetrical pyridine-2,6-dicarboxylamide oligoamide foldamers with varying lengths and substituents at the end groups were synthetized to study their conformational properties and folding patterns. The @-type folding pattern resembled the oxyanion-hole motifs of enzymes, but several alternative folding patterns could also be characterized. Computational studies revealed several alternative conformers of nearly equal stability. These folding patterns differed from each other in their intramolecular hydrogen-bonding patterns and aryl-aryl interactions. In the solid state, the foldamers adopted either the globular @-type fold or the more extended S-type conformers, which were very similar to those foldamers obtained computationally. In some cases, the same foldamer molecule could even crystallize into two different folding patterns, thus confirming that the different folding patterns are very close in energy in spite of their completely different shapes. Finally, the best match for the observed NOE interactions in the liquid state was a conformation that matched the computationally characterized helix-type fold.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Folding Patterns in a Family of Oligoamide Foldamers

Kortelainen

Suhonen

Hamza

et al. 2015

Chemistry A European J

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“…In our previous studies, we investigated the conformational variance of a series of oligoamide foldamers by computational, single crystal X-ray diffraction and NMR spectroscopic methods. 19,20 The oligoamide foldamers were able to adopt a conformation -among other almost equally stable conformers -where three intramolecular hydrogen bonds are formed to single carbonyl oxygen, closely resembling an oxyanion hole motif found in the active sites of enzymes 21 . In enzymes, an oxyanion hole motif consists of two or more hydrogen bond donors, which can form hydrogen bonds to a negatively charged oxygen atom of a reaction intermediate thus stabilising it and lowering the energy cost of the reaction.…”

Section: Introductionmentioning

confidence: 99%

Conformational properties and folding analysis of a series of seven oligoamide foldamers

et al. 2016

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33 crystal structures (11 unsolvated and 22 solvates) of a series of seven oligoamide foldamers were analysed. The crystal structures revealed that despite the structural and environmental differences the series of foldamers prefer only two general conformations, a protohelical @-conformation and a sigmoidal S-conformation. Both conformations also have preferred crystal packing motifs and solvate forming tendencies. Hydrogen bonding was found to be the most decisive factor in conformational preference, but steric properties, the type of the peripheral substituents, as well as solvent and aromatic interactions were also found to have an effect on the conformational details and crystal form.

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“…CCDC reference numbers 885902-885911 See DOI: 10.1039/b000000x/ groups are also preorganized to stabilize the negatively charged intermediate, which in addition decreases the entropic energy cost 50 of the reaction. 4 Examples of this catalytic effect include serineprotease 5 and triglyceride hydrolysis by cutinase 6 .…”

Section: Introductionmentioning

confidence: 99%

“…The 2-DMSO I solvate has two intramolecular hydrogen bonds with an S(7) motif similarly to the 2-form I, but both of these 25 bonds are formed between the inner C=O groups (2, 3) and the outer N-H groups (1,4). Therefore, the molecule has a more open conformation than 2-form I (Fig.…”

mentioning

confidence: 99%