scholarly journals Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

2009 ◽  
Vol 5 (6) ◽  
pp. 1524-1544 ◽  
Author(s):  
Claudio A. Morgado ◽  
Petr Jurečka ◽  
Daniel Svozil ◽  
Pavel Hobza ◽  
Jiří Šponer
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Basis Set ◽  
Base Stacking ◽  
Acid Base ◽  
Complete Basis ◽  
Nucleic Acid Base ◽  
Complete Basis Set ◽  
Complete Basis Set Limit

scholarly journals An optimized charge penetration model for use with the AMOEBA force field

2017 ◽  
Vol 19 (1) ◽  
pp. 276-291 ◽  
Author(s):  
Joshua A. Rackers ◽  
Qiantao Wang ◽  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Ligand Binding ◽  
Force Field ◽  
Short Range ◽  
Electrostatic Model ◽  
Base Stacking ◽  
Acid Base ◽  
Nucleic Acid Base ◽  
Range Error ◽  
Amoeba Force Field

Inclusion of charge penetration corrects the short-range error in the electrostatic model of the AMOEBA force field, and improves the accuracy of interactions ranging from nucleic acid base stacking to protein–ligand binding.

Finding and visualizing nucleic acid base stacking

1996 ◽  
Vol 14 (1) ◽  
pp. 6-11 ◽  
Author(s):  
H.A. Gabb ◽  
S.R. Sanghani ◽  
C.H. Robert ◽  
C. Prévost
Keyword(s):  
Nucleic Acid ◽  
Base Stacking ◽  
Acid Base ◽  
Nucleic Acid Base

From CCSD(T)/aug-cc-pVTZ-J to CCSD(T) complete basis set limit isotropic nuclear magnetic shieldings via affordable DFT/CBS calculations

2011 ◽  
Vol 49 (5) ◽  
pp. 231-236 ◽  
Author(s):  
Teobald Kupka ◽  
Michał Stachów ◽  
Marzena Nieradka ◽  
Jakub Kaminsky ◽  
Tadeusz Pluta ◽  
...  
Keyword(s):  
Basis Set ◽  
Complete Basis ◽  
Complete Basis Set ◽  
Complete Basis Set Limit ◽  
Nuclear Magnetic
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