scholarly journals Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

2011 ◽  
Vol 7 (9) ◽  
pp. 2886-2902 ◽  
Author(s):  
Marie Zgarbová ◽  
Michal Otyepka ◽  
Jiří Šponer ◽  
Arnošt Mládek ◽  
Pavel Banáš ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical

Evaluation of Chemotherapeutic Activity of the Selected Bases’ Analogues of Nucleic Acids Supported by ab initio Various Quantum Chemical Calculations

2020 ◽  
Vol 16 (2) ◽  
pp. 93-103 ◽  
Author(s):  
Piotr Kawczak ◽  
Leszek Bober ◽  
Tomasz Bączek
Keyword(s):  
Biological Activity ◽  
Nucleic Acids ◽  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Structural Parameters ◽  
Principal Component ◽  
Polarizable Continuum Model ◽  
Activity Data ◽  
Qsar Models

Background: Pharmacological and physicochemical classification of bases’ selected analogues of nucleic acids is proposed in the study. Objective: Structural parameters received by the PCM (Polarizable Continuum Model) with several types of calculation methods for the structures in vacuo and in the aquatic environment together with the huge set of extra molecular descriptors obtained by the professional software and literature values of biological activity were used to search the relationships. Methods: Principal Component Analysis (PCA) together with Factor Analysis (FA) and Multiple Linear Regressions (MLR) as the types of the chemometric approach based on semi-empirical ab initio molecular modeling studies were performed. Results: The equations with statistically significant descriptors were proposed to demonstrate both the common and differentiating characteristics of the bases' analogues of nucleic acids based on the quantum chemical calculations and biological activity data. Conclusion: The obtained QSAR models can be used for predicting and explaining the activity of studied molecules.

Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds

2019 ◽  
Vol 75 (3) ◽  
pp. 301-309
Author(s):  
Jelena M. Andrić ◽  
Ivana M. Stanković ◽  
Snežana D. Zarić
Keyword(s):  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Nucleic Acids ◽  
Metal Ions ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Metal Ion ◽  
Water Molecules ◽  
Nucleic Acid Bases ◽  
Coordinated Water

The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.

A general intermolecular force field based on tight-binding quantum chemical calculations

2017 ◽  
Vol 147 (16) ◽  
pp. 161708 ◽  
Author(s):  
Stefan Grimme ◽  
Christoph Bannwarth ◽  
Eike Caldeweyher ◽  
Jana Pisarek ◽  
Andreas Hansen
Keyword(s):  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Tight Binding ◽  
Intermolecular Force

Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides†

2001 ◽  
Vol 105 (28) ◽  
pp. 6474-6487 ◽  
Author(s):  
George A. Kaminski ◽  
Richard A. Friesner ◽  
Julian Tirado-Rives ◽  
William L. Jorgensen
Keyword(s):  
Force Field ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical
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