scholarly journals Impact of Geometry Optimization on Base–Base Stacking Interaction Energies in the Canonical A- and B-Forms of DNA

2013 ◽  
Vol 117 (7) ◽  
pp. 1560-1568 ◽  
Author(s):  
Ashley Ringer McDonald ◽  
Elizabeth J. Denning ◽  
Alexander D. MacKerell
Keyword(s):  
Geometry Optimization ◽  
Interaction Energies ◽  
Base Stacking ◽  
Stacking Interaction

Ion solvation by dipolar aprotic solvents. An ab initio study

1987 ◽  
Vol 52 (1) ◽  
pp. 6-13 ◽  
Author(s):  
Petr Kyselka ◽  
Zdeněk Havlas ◽  
Ivo Sláma
Keyword(s):  
Ab Initio ◽  
Geometry Optimization ◽  
Molecular Structures ◽  
Dimethyl Sulphoxide ◽  
Ion Solvation ◽  
Interaction Energies ◽  
Ab Initio Study ◽  
Solvation Energies ◽  
Dipolar Aprotic Solvents ◽  
Complete Geometry Optimization

The paper deals with the solvation of Li+, Be2+, Na+, Mg2+, and Al3+ ions in dimethyl sulphoxide, dimethylformamide, acetonitrile, and water. The ab initio quantum chemical method was used to calculate the solvation energies, molecular structures, and charge distributions for the complexes water···ion, acetonitrile···ion, dimethyl sulphoxide···ion, and dimethylformamide···ion. The interaction energies were corrected for the superposition error. Complete geometry optimization was performed for the complex water···ion. Some generalizations are made on the basis of the results obtained.

An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking

Biopolymers ◽  
1978 ◽  
Vol 17 (10) ◽  
pp. 2341-2360 ◽  
Author(s):  
Rick L. Ornstein ◽  
Robert Rein ◽  
Donnal L. Breen ◽  
Robert D. Macelroy
Keyword(s):  
Nucleic Acid ◽  
Potential Function ◽  
Interaction Energies ◽  
Acid Interaction ◽  
Base Stacking

The nonadditivity of stacking interactions in adenine–thymine and guanine–cytosine stacked structures: Study by MP2 and SCS-MP2 calculations

2015 ◽  
Vol 14 (05) ◽  
pp. 1550037 ◽  
Author(s):  
Chang-Liang Sun ◽  
Fu Ding ◽  
Yan-Li Ding ◽  
Chang-Sheng Wang
Keyword(s):  
Basis Sets ◽  
Negative Cooperativity ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Base Pairs ◽  
Stacking Interaction ◽  
Mp2 Calculations ◽  
Calculation Results ◽  
Intermolecular Distances ◽  
Adenine Thymine

The nonadditivity of stacking interactions in stacked structures of adenine–thymine and guanine–cytosine base pairs is investigated by MP2 and SCS-MP2 calculations with 6-311++G** and aug-cc-pvdz basis sets. The calculation results indicate that the intermolecular distances in the multi-stacked structures do not become shorter obviously as the stacked structure added. The middle stacking interaction energies in the multi-stacked structures also become weaker than that of dimer structures. It is found that the total stacking interaction energies of the trimer and tetramer stacked structures do not increase proportionally. Based on the results, we suggest that there is negative cooperativity of the stacking interactions in the adenine–thymine and guanine–cytosine stacked structures.

Converting SMILES to Stacking Interaction Energies

2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Steven Wheeler
Keyword(s):  
Quantum Chemical ◽  
Density Functional ◽  
Computational Cost ◽  
Aromatic Amino Acids ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Structure Based Drug Design ◽  
Stacking Interaction ◽  
Large Sets ◽  
Quantum Chemical Computations

<p>Predicting the strength of stacking interactions involving heterocycles is vital for several fields, including structure-based drug design. While quantum chemical computations can provide accurate stacking interaction energies, these come at a steep computational cost. To address this challenge, we recently developed quantitative predictive models of stacking interactions between drug-like heterocycles and the aromatic amino acids Phe, Tyr, and Trp (DOI: 10.26434/chemrxiv.7628939.v4). These models depend on heterocycle descriptors derived from electrostatic potentials (ESPs) computed using density functional theory and provide accurate stacking interactions without the need for expensive computations on stacked dimers. Herein, we show that these ESP-based descriptors can be reliably evaluated directly from the atom connectivity of the heterocycle, providing a means of predicting both the descriptors and the potential for a given heterocycle to engage in stacking interactions without resorting to any quantum chemical computations. This enables the conversion of simple molecular representations (<i>e.g</i>. SMILES) directly into accurate<i> </i>stacking interaction energies using a freely-available online tool, thereby providing a way to rapidly rank the stacking abilities of large sets of heterocycles.</p> <p> </p>

Converting SMILES to Stacking Interaction Energies

2019 ◽  
Vol 59 (8) ◽  
pp. 3413-3421 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Steven E. Wheeler
Keyword(s):  
Interaction Energies ◽  
Stacking Interaction
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