scholarly journals Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins

2015 ◽  
Vol 11 (4) ◽  
pp. 1854-1863 ◽  
Author(s):  
Arghya Barman ◽  
Bruce Batiste ◽  
Donald Hamelberg
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Π Interactions

Hydration of platinum(II) complexes: a molecular mechanics study using atom-based force-field parameters

2000 ◽  
Vol 104 (3-4) ◽  
pp. 247-251 ◽  
Author(s):  
Jacqueline Langlet ◽  
Jacqueline Berg�s ◽  
Jacqueline Caillet ◽  
Jiri Kozelka
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Force Field Parameters

The tetracycline: Mg2+ complex: A molecular mechanics force field

2006 ◽  
Vol 27 (13) ◽  
pp. 1517-1533 ◽  
Author(s):  
Alexey Aleksandrov ◽  
Thomas Simonson
Keyword(s):  
Force Field ◽  
Molecular Mechanics

AFMM: A molecular mechanics force field vibrational parametrization program

2005 ◽  
Vol 167 (1) ◽  
pp. 34-42 ◽  
Author(s):  
A.C. Vaiana ◽  
Z. Cournia ◽  
I.B. Costescu ◽  
J.C. Smith
Keyword(s):  
Force Field ◽  
Molecular Mechanics

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.

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