Basis set effect on hydrogen bond stabilization energy estimation of the Watson–Crick type nucleic acid base pairs using medium-size basis sets: single point MP2 evaluations at the HF optimized structures

2000 ◽  
Vol 2 (13) ◽  
pp. 2869-2872 ◽  
Author(s):  
Shun-ichi Kawahara ◽  
Tadafumi Uchimaru
Keyword(s):  
Single Point ◽  
Stabilization Energy ◽  
Basis Set ◽  
Basis Sets ◽  
Medium Size ◽  
Acid Base ◽  
Base Pairs ◽  
Energy Estimation ◽  
Basis Set Effect ◽  
Nucleic Acid Base

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.

scholarly journals The World of Non-Covalent Interactions: 2006

2006 ◽  
Vol 71 (4) ◽  
pp. 443-531 ◽  
Author(s):  
Pavel Hobza ◽  
Rudolf Zahradník ◽  
Klaus Müller-Dethlefs
Keyword(s):  
Nucleic Acid ◽  
Ab Initio ◽  
Molecular Clusters ◽  
Medium Size ◽  
Acid Base ◽  
Energy Potential ◽  
Base Pairs ◽  
Nucleic Acid Base ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.

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