Abstract
Monte Carlo simulations are presented for the bases A, C, G, T, and U enclosed in a cluster of forty water molecules and for the base pairs A–T, G–C, and A–U enclosed in a cluster of fifty water molecules. These computations are carried out at a simulated temperature of 300 K. The importance of the temperature effect is shown by carrying the MC simulation for adenine at T=100 K. The intermolecular interactions are computed with atom–atom pair potentials obtained from quantum-mechanical calculations on the water–water and water–base complexes. The identification of the positions and orientations for the water molecules in the first hydration shell is obtained from hydrogen and oxygen atoms probability distribution maps. Relations between the water structure around the bases and base pairs and the water structure in the major and minor groove of B-DNA double helix are preliminarily presented.
Keywords
MoleculeChemistryIntermolecular forceHydrogen bondSolvation shellMonte Carlo methodCluster (spacecraft)Base pairBase (topology)Water clusterCrystallographyHydrogen atomAtom (system on chip)Chemical physicsComputational chemistryDNAGroup (periodic table)SolvationOrganic chemistry
Affiliated Institutions
Related Publications
Comparison of simple potential functions for simulating liquid water
Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for t...
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
Abstract A first‐generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic har...
Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model
A new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented. It allows Hartree−Fock (HF), density functional (DF) and pos...
Development and testing of a general amber force field
Abstract We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic a...
Constant temperature molecular dynamics calculation on Lennard-Jones fluid and its application to watera)
Constant temperature molecular dynamics calculation has been carried out on Lennard-Jones liquid simulating argon. This method, proposed recently by Andersen, intends to transfo...
Publication Info
- Year
- 1980
- Type
- article
- Volume
- 72
- Issue
- 7
- Pages
- 3979-3992
- Citations
- 84
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
84
OpenAlex
Cite This
E. Clementi,
G. Corongiu
(1980).
A theoretical study on the water structure for nucleic acids bases and base pairs in solution at T=300 K.
The Journal of Chemical Physics
, 72
(7)
, 3979-3992.
https://doi.org/10.1063/1.439676
Identifiers
- DOI
- 10.1063/1.439676