The use of the AMBER force field in conformational analysis of carbohydrate molecules: Determination of the solution conformation of methyl ?-lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations

Biopolymers ◽  
1995 ◽  
Vol 35 (1) ◽  
pp. 55-73 ◽  
Author(s):  
Juan Luis Asensio ◽  
Jesus Jimenez-Barbero
Keyword(s):  
Nmr Spectroscopy ◽  
Conformational Analysis ◽  
Force Field ◽  
Molecular Mechanics ◽  
Solution Conformation ◽  
Amber Force Field

Plural Origins of Molecular Homochirality in Our Biota Part II. The Relative Stabilities of Homochiral and Mixed Oligoribotides and Peptides

1997 ◽  
Vol 52 (1-2) ◽  
pp. 89-96 ◽  
Author(s):  
Thereza Amélia Soares ◽  
Roberto Dias Lins ◽  
Ricardo Longo ◽  
Richard Garratt ◽  
Ricardo Ferreira
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Force Field ◽  
Molecular Mechanics ◽  
Computer Simulations ◽  
The Other ◽  
Amino Acid Residues ◽  
Relative Stabilities ◽  
Amber Force Field ◽  
Cross Inhibition

Abstract By computer simulations -molecular mechanics and molecular dynamics with the amber force field (Weiner et al., (1986), J. Comp. Chem. 7, 2 30-252) -we have determined the stabilities of oligoribotide strands built with ᴅ -and ʟ-riboses, and of peptide chains with ᴅ -and ʟ-amino acid residues. In particular, complementary double-chains of oligoribotides were studied, since they are an important feature of the growing mechanism of modern nucleic acids. Peptide chains on the other hand, grow without need of a template. We found that mixed oligoribotides are less stable than homochiral ones, and that this chiral effect is less noticeable in peptide chains. The results support the interpretation that ʟ-riboses act as terminators to the template-assisted growth of oligo-r-Gᴅ (enantiomeric cross-inhibition; Joyce et al., (1987), Proc. Natl. Acad. Sci. USA 84, 4398-4402). Based on this effect, a chemical pathway is proposed which could, under assumed prebiotic conditions, bypass the hindrance of homochiral growth.

Conformational analysis of [Cpp1, Sar7, Arg8] vasopressin by 1H-NMR spectroscopy and molecular mechanics calculations

2009 ◽  
Vol 38 (6) ◽  
pp. 528-538 ◽  
Author(s):  
MARK D. SHENDEROVICH ◽  
FRANCISZEK KASPRZYKOWSKI ◽  
ADAM LIWO ◽  
ILMARS SEKACIS ◽  
JURIS SAULITIS ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Conformational Analysis ◽  
Molecular Mechanics ◽  
1H Nmr ◽  
1H Nmr Spectroscopy ◽  
Molecular Mechanics Calculations

Synthèse, structure et études spectroscopiques RMN 1H et 13C de dérivés perhydrocyclododéca[b]furaniques

1991 ◽  
Vol 69 (3) ◽  
pp. 521-527 ◽  
Author(s):  
Michel Albrand ◽  
René Dolmazon ◽  
Patrick Pollet
Keyword(s):  
Conformational Analysis ◽  
Force Field ◽  
Key Words ◽  
Molecular Mechanics ◽  
Trans Isomer ◽  
Nmr Spectra ◽  
Synthetic Route ◽  
Force Field Calculations ◽  
Cis Isomer ◽  
C Nmr

A synthetic route to perhydrocyclododeca[b]furan-3-ols, perhydrocyclododeca[b]furan-3-ones, and perhydrocyclododeca[b]furan derivatives is described. Their configurations were determined. For the perhydrocyclododeca[b]furan-3-one and perhydrocyclododeca[b]furan pairs, the cis isomer was much less stable than the trans isomer. This agrees well with results from a conformational analysis, carried out by molecular mechanics. The 1H and l3C NMR spectra are reported. Key words: perhydrocyclododeca[b]furans, conformations, force field calculations, 1H and 13C NMR.

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