Can We Predict the Conformational Preference of Amides?

Авалос, M.; Babiano, Reyes; Barneto, José Luis; Bravo, José; Cintas, Pedro; Jiménez, José L.; Palacios, Juan C.

doi:10.1021/jo0102361

Cited by 49 publications

(48 citation statements)

References 82 publications

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“…The conformational equilibrium of N-methylformamide and N-methylacetamide is shifted to the Z-conformer [1,3,[11][12][13]. This can be explained by steric interactions between the carbonyl group and the methyl nitrogen.…”

Section: Introductionmentioning

confidence: 99%

“…This can be explained by steric interactions between the carbonyl group and the methyl nitrogen. Computational methods have been shown to be adequate for the study of the conformational equilibrium of these compounds [10,[13][14][15][16][17][18][19][20][21][22][23] by providing results in accordance with experimental data [1-3, 5-7, 9, 11-13, 15-20, 24-26].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

N‐arylamides and N‐arylcarbamates NCO internal rotation barrier study by molecular modeling

Grasel¹,

Oliveira²,

Fontoura³

et al. 2011

Int J of Quantum Chemistry

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Amides and carbamates present an energetic barrier associated to NAC(O) bond rotation, which determines two different equilibrium geometries. In this work, the conformational equilibrium of formanilide, acetanilide, methyl and t-butyl phenylcarbamates, and their N-methylderivatives was studied by AM1 and B3LYP/6-31G(d,p) calculations. The effect of aryl p-substituents (MeO, Me, Cl, Br, CN, and NO 2 ) was also studied. Amide barriers were found by DFT calculation between 12 and 21 kcal/ mol. Carbamates, on the other hand, showed barriers between 11 and 15 kcal/mol. AM1 underestimates the energetic barriers and provides values around half those obtained by B3LYP/6-31G(d,p) calculations. Electron withdrawing substituents on aryl group decrease the barrier.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

N‐arylamides and N‐arylcarbamates NCO internal rotation barrier study by molecular modeling

Grasel¹,

Oliveira²,

Fontoura³

et al. 2011

Int J of Quantum Chemistry

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“…Intramolecular aromatic stacking above and below the xylylene unit as observed in the compact solid-state conformation certainly influences torsion angles about C ␣ -N and C ␣ -C aryl bonds. The intrinsic conformational preferences of these bonds, which also define the helix propensity of this monomer, result from a combination of steric, electrostatic, and hyperconjugation effects as calculated for smaller benzylic structures (24,25).…”

Section: Resultsmentioning

confidence: 99%

Probing helix propensity of monomers within a helical oligomer

Dolain

Léger

Delsuc

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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A simple strategy is proposed to assess the propensity of a given monomer to follow or not follow a particular helical scheme and to study helix reversal phenomena within helical oligomers. It consists of placing a monomer having a low helix propensity between two conformationally stable helical segments. Helix reversion then occurs preferentially at the site of this monomer, leading to the formation of isomers having P (right-handed) or M (left-handed) helicities at each of the two helical segments. The proportion between the P-P͞M-M and P-M isomers is indicative of the stereochemical relations between the inserted monomer and the helical frame. Thus, xylylene or carboxylic acid anhydride spacers have been introduced between two helical oligoamides of 8-amino-2-quinolinecarboxylic acid. Both these spacers presumably lack some of the structural features that confer quinoline units with a high helix propensity. Only one species is observed in solution in the case of an anhydride spacer. This species was shown by x-ray crystallography to be a racemic mixture of P-P and M-M helices. Unexpectedly, the anhydride is consistently incorporated within helical oligoamides. For the xylylene spacer, the P-P͞M-M racemate and P-M meso compound are in equal proportions in chloroform, showing that this spacer does not have a propensity to adopt any helical conformation in this solvent. However, the equilibria between the various isomers are shifted in toluene, where one species largely prevails. This species was shown by x-ray crystallography to be the P-P͞M-M racemate. Molecular dynamics simulations are consistent with these solution data.conformation analysis ͉ folding ͉ helices M olecular helices are one of the major structural motifs of natural and synthetic polymers and oligomers (1-7). A fundamental property of a molecular helix is the average length over which it keeps its right-handed (P) or left-handed (M) integrity: the length over which neither uncoiling nor reversal of helix handedness occurs. This parameter is important in structural biology because it reflects the stability of, for example, ␣-helical peptides; it is also important in material science because it determines the limit of chiral amplification that a given helical polymeric chain may reach (1, 6). Helical integrity may also be useful to remotely control the stereochemistry of a reaction (8). For example, in a helical polymer, a single chiral residue may induce a local conformational preference for a particular handedness. This local preference is propagated and amplified by the helical integrity of the polymer until a partial uncoiling or helix reversal occurs. The average length over which a helix handedness keeps its integrity is determined by a combination of local conformational preferences in the helix backbone as well as intramolecular and solvent-driven interactions that define the helix propensity associated with the monomers (1-7). Long-range intermolecular helix-helix interactions and helix bundling have also been shown contribute to helix st...

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“…[30 -33] This two-step methodology was employed in amide conformational analysis with good accomplishment and feasible computational time. [34] …”

Section: Methodsmentioning

confidence: 99%

Anisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluation

Gonçalves

Esteves

Pinto

et al. 2008

Magnetic Reson in Chemistry

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Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental (1)H and (13)C NMR (in CDCl(3), CD(3)OD, and DMSO-d(6) solvents) and in some cases with good correlation to theoretical (1)H and (13)C NMR DFT-GIAO (B3LYP/6-311++G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an N-CH(2) moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied.

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Can We Predict the Conformational Preference of Amides?

Cited by 49 publications

References 82 publications

N‐arylamides and N‐arylcarbamates NCO internal rotation barrier study by molecular modeling

N‐arylamides and N‐arylcarbamates NCO internal rotation barrier study by molecular modeling

Probing helix propensity of monomers within a helical oligomer

Anisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluation

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