Estimating the "steric clash" at cis peptide bonds

Journal of Physical Chemistry B

Volumn 112, Issue 26, 2008, Pages 7894-7902

  Mathieu, Simon ^a   Poteau, Romuald ^b   Trinquier, Georges ^b  

^a Université Paul Sabatier   (France)

^b INSA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; NETWORK PROTOCOLS; SEPARATION;

DIHEDRAL ANGLES; ENERGY ANALYSIS; ENERGY COSTS; LATERAL CHAINS; PEPTIDE BONDS;

AMINES;

HYDROCARBON; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY;

HYDROCARBONS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PEPTIDES;

EID: 47749086992     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp711082d     Document Type: Article

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66. Seeing NEP as 1,4-dimethyl N-methylacetamide, the amide main frame can adopt trans or cis arrangements (E or Z stereoisomers, respectively). With respect to this main frame, the terminal methyl groups keep in both cases a synclinal gauche conformation, but this corresponds to clear trans and cis positions relative to each other, as can be seen in Figure 1. This is why we will use the simple labelling tt and cc.
67. Seeing n-hexane as 1,4-dimethyl n-butane, the main frame is fixed here in anti-periplanar and syn-periplanar conformations (sometimes improperly designated as s-trans or s-cis, respectively). With respect to this main frame, the terminal methyl groups again keep a synclinal gauche position in both cases, and it appears from Figure 2 that they assume trans and cis relative orientations, respectively. For the sake of comparison, we will therefore keep a tt and cc labelling, while the strict designations are gag and gsg, respectively.
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72. Strictly speaking, the bond separation energy (BSE) would correspond to the opposite way in equations (1) and (2). As written here, their energies should be designed as bond association energies (BAE). We choose to keep the former widespread acronym. Positive BSE therefore means the bonds are unstabilized when combined.
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75. These effects deserve to be studied elsewhere, the present work only address the steric effects.