Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a ◽  
Author(s):  
Jiří Šponer ◽  
Judit E. Šponer ◽  
Arnošt Mládek ◽  
Petr Jurečka ◽  
Pavel Banáš ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Molecular Mechanics ◽  
Base Stacking ◽  
Dna And Rna

Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry

2004 ◽  
Vol 108 (4) ◽  
pp. 621-627 ◽  
Author(s):  
George A. Kaminski ◽  
Harry A. Stern ◽  
B. J. Berne ◽  
Richard A. Friesner
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Ab Initio ◽  
Molecular Mechanics

Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.

2015 ◽  
Vol 119 (30) ◽  
pp. 9477-9495 ◽  
Author(s):  
Nohad Gresh ◽  
Judit E. Sponer ◽  
Mike Devereux ◽  
Konstantinos Gkionis ◽  
Benoit de Courcy ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Molecular Mechanics ◽  
Intermolecular Interaction ◽  
Interaction Energies

Carrier mobility in double-helix DNA and RNA: A quantum chemistry study with Marcus-Hush theory

2016 ◽  
Vol 145 (23) ◽  
pp. 235101 ◽  
Author(s):  
Tao Wu ◽  
Lei Sun ◽  
Qi Shi ◽  
Kaiming Deng ◽  
Weiqiao Deng ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Carrier Mobility ◽  
Double Helix ◽  
Dna And Rna

Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA

2003 ◽  
Vol 107 (33) ◽  
pp. 8669-8681 ◽  
Author(s):  
Nohad Gresh ◽  
Judit E. Šponer ◽  
Nad'a Špačková ◽  
Jerzy Leszczynski ◽  
Jiři Šponer
Keyword(s):  
Molecular Mechanics ◽  
Theoretical Study ◽  
Guanosine Monophosphate ◽  
Dna And Rna

The role of electron donors and acceptors in base stacking in DNA and RNA

1990 ◽  
Vol 171 (1) ◽  
pp. 97-101 ◽  
Author(s):  
E.C.M. Chen ◽  
E.S.D. Chen ◽  
W.E. Wentworth
Keyword(s):  
Electron Donors ◽  
Base Stacking ◽  
Dna And Rna

Quantum chemistry and molecular mechanics studies of the lamella structure of hydrotalcite with Mg/Al ratio of 3

2008 ◽  
Vol 69 (5-6) ◽  
pp. 1066-1069 ◽  
Author(s):  
Min Pu ◽  
Yu-Li Wang ◽  
Ling-Yan Liu ◽  
Ya-Hui Liu ◽  
Jing He ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Molecular Mechanics ◽  
Lamella Structure

scholarly journals FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models

2013 ◽  
Author(s):  
Anders Steen Christensen ◽  
Thomas Hamelryck ◽  
Jan H Jensen
Keyword(s):  
Quantum Chemistry ◽  
Force Field ◽  
Molecular Mechanics ◽  
Side Chain ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Model Peptide ◽  
Quantum Chemistry Calculations ◽  
Set Up ◽  
Model Structures

We present a powerful Python library to quickly and efficiently generate realistic peptide model structures. The library makes it possible to quickly set up quantum mechanical calculations on model peptide structures. It is possible to manually specify a specific conformation of the peptide. Additionally the library also offers sampling of backbone conformations and side chain rotamer conformations from continuous distributions. The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library. Finally, it is possible to output the resulting structures directly to files in XYZ and PDB formats, or optionally directly as input files for a quantum chemistry program. FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license.

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