Hydrogen-Bonded Nucleic Acid Base Pairs Containing Unusual Base Tautomers:  Complete Basis Set Calculations at the MP2 and CCSD(T) Levels

2007 ◽  
Vol 111 (3) ◽  
pp. 641-645 ◽  
Author(s):  
Jaroslav Rejnek ◽  
Pavel Hobza
Keyword(s):  
Nucleic Acid ◽  
Basis Set ◽  
Acid Base ◽  
Base Pairs ◽  
Complete Basis ◽  
Nucleic Acid Base ◽  
Complete Basis Set ◽  
Hydrogen Bonded

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

A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs

2005 ◽  
Vol 1 (6) ◽  
pp. 1275-1285 ◽  
Author(s):  
Timothy J. Giese ◽  
Edward C. Sherer ◽  
Christopher J. Cramer ◽  
Darrin M. York
Keyword(s):  
Nucleic Acid ◽  
Quantum Model ◽  
Acid Base ◽  
Base Pairs ◽  
Nucleic Acid Base ◽  
Hydrogen Bonded

COMPUTATION OF LARGE SYSTEMS WITH AN ECONOMIC BASIS SET: AB INITIO CALCULATIONS OF BIOLOGICAL NUCLEIC ACID BASE PAIRS

2006 ◽  
Vol 05 (spec01) ◽  
pp. 411-420 ◽  
Author(s):  
WENJIE FAN ◽  
RUIQIN ZHANG
Keyword(s):  
Nucleic Acid ◽  
Single Point ◽  
Basis Set ◽  
Basis Sets ◽  
Mulliken Charge ◽  
Acid Base ◽  
Base Pairs ◽  
Point Energy ◽  
Economic Basis ◽  
Nucleic Acid Base

We show that an economic basis set, in which the polarization functions are considered only for oxygen and nitrogen atoms of strong electronegativity, can be used to determine reliable structures of nucleic acid base pairs. Mulliken charge analysis and the HOMO-LUMO gap in single-point energy calculations using standard basis sets on the geometric structures optimized with the economic basis set found reasonable agreements with the ones of standard calculations. This study is expected to provide a general guideline for basis set selection in the computation of large biological systems being performed with considerable high accuracy, using a low cost computation resource.

ChemInform Abstract: Hydrogen-Bonded and Stacked Homo- and Heterodimers of Systems Modeling Nucleic Acid Base Pairs

ChemInform ◽  
2010 ◽  
Vol 31 (12) ◽  
pp. no-no
Author(s):  
A. M. Plokhotnichenko ◽  
E. D. Radchenko ◽  
S. G. Stepanian ◽  
L. Adamowicz
Keyword(s):  
Nucleic Acid ◽  
Systems Modeling ◽  
Acid Base ◽  
Base Pairs ◽  
Nucleic Acid Base ◽  
Hydrogen Bonded
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