Quantum-Mechanical Investigations of the Electronic Structure of Nucleic Acids and Their Constituents

1969 ◽  
pp. 327-402 ◽  
Author(s):  
Bernard Pullman ◽  
Alberte Pullman
Keyword(s):  
Electronic Structure ◽  
Nucleic Acids ◽  
Quantum Mechanical

Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions

2015 ◽  
Vol 17 (2) ◽  
pp. 1399-1410 ◽  
Author(s):  
Holger Kruse ◽  
Jiří Šponer
Keyword(s):  
Electronic Structure ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Penalty Function ◽  
Geometry Optimization ◽  
Quantum Mechanical ◽  
Structural Motifs ◽  
Mechanical Methods ◽  
Structure Geometry

Flexible biomolecular structures can be optimized by quantum mechanical methods in a highly controllable manner using penalty function restraints to prevent non-native conformations.

scholarly journals Quantum algorithm for alchemical optimization in material design

2021 ◽  
Author(s):  
Panagiotis Kl. Barkoutsos ◽  
Fotios Gkritsis ◽  
Pauline J. Ollitrault ◽  
Igor O. Sokolov ◽  
Stefan Woerner ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Drug Discovery ◽  
Chemical Composition ◽  
Quantum Algorithm ◽  
Material Design ◽  
Quantum Mechanical ◽  
Near Future

‘Alchemical’ quantum algorithm for the simultaneous optimisation of chemical composition and electronic structure for material design. By exploiting quantum mechanical principles this approach will boost drug discovery in the near future.

Quantum-theoretical approaches to proteins and nucleic acids

2017 ◽  
Author(s):  
Mauro Boero ◽  
Masaru Tateno
Keyword(s):  
Nucleic Acids ◽  
Density Functional ◽  
A Priori ◽  
Alternative Methods ◽  
Parallel Tempering ◽  
Quantum Mechanical ◽  
Chemical Bonds ◽  
Functional Theory ◽  
Hartree Fock ◽  
Theoretical Approaches

This article describes quantum methods used to study proteins and nucleic acids: Hartree–Fock all-electron approaches, density-functional theory approaches, and hybrid quantum-mechanics/molecular-mechanics approaches. In addition to an analysis of the electronic structure, quantum-mechanical approaches for simulating proteins and nucleic acids can elucidate the cleavage and formation of chemical bonds in biochemical reactions. This presents a computational challenge, and a number of methods have been proposed to overcome this difficulty, including enhanced temperature methods such as high-temperature molecular dynamics, parallel tempering and replica exchange. Alternative methods not relying on the knowledge a priori of the final products make use of biasing potentials to push the initial system away from its local minimum and to enhance the sampling of the free-energy landscape. This article considers two of these biasing techniques, namely Blue Moon and metadynamics.

scholarly journals Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

2008 ◽  
Vol 112 (27) ◽  
pp. 8188-8197 ◽  
Author(s):  
Daniel Svozil ◽  
Judit E. Šponer ◽  
Ivan Marchan ◽  
Alberto Pérez ◽  
Thomas E. Cheatham ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Nucleic Acids ◽  
Sugar Phosphate ◽  
Phosphate Backbone
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