This page contains general information about the DFT Database
for RNA Catalysis. Click on any of the following links:
Following is a list of definitions of electronic
and thermodynamic quantities computed for each molecular structure in the
database.
Definitions of Thermodynamic
Quantities |
|
E | Electronic plus nuclear energy |
Eelec | Electronic energy |
ENN | Nuclear-nuclear repulsion energy |
E0 | Zero-point energy |
EZPV | Zero-point vibrational energy |
Evib | Thermal vibrational energy correction |
Erot | Rotational energy |
Etrans | Translational energy |
U |
Internal energy |
H |
Enthalpy |
S |
Entropy |
G |
Gibbs free energy (in the gas phase) |
Gaq |
Gibbs free energy (in solution) |
ΔGsol |
Solvation free energy |
T |
Absolute temperature |
R |
Universal gas constant |
Definition of Electronic properties |
|
|D| |
Dipole moment |
alpha |
Isotropic polarizability |
qi |
Atomic charge (NBO and CHelpG) |
phi(r) |
Electrostatic potential surface |
IP |
1st ionization potential (Koopman approximation) |
EA |
1st electron affinity (Koopman approximation) |
nui |
Vibrational frequency |
Based on initial tests for reactions involving anions, first-generation database
is based on gas-phase optimized structures using Kohn-Sham density-functional
theory with hybrid Becke three parameter exchange functional [1,2]and
Lee, Yang, Parr correlation functional [3](B3LYP)
with the 6-31++G(d,p) basis set. Stability and frequency check is made at
the same level to make sure that a stable minimum have been reached. Thermodynamic
quantities such as the zero-point vibrational energy, thermal vibrational
contributions to enthalpy, entropy and Gibbs free energy is also evaluated
by frequency calculations. Electronic energies and other properties, including
dipole moments, atomic charges and polarizabilities, are refined via single
point calculations at the optimized geometries using the larger 6-311++G(3df,2p)
basis set with 'tight' convergence criteria to ensure high precision for properties
sensitive to the use of diffuse basis functions. The zero-point energy and
other thermal energy corrections obtained from the frequency calculation are
used to adjust the single point electronic energy to get the free energy and
other thermodynamic quantities. All of the calculations will be implemented
with GAUSSIAN03 package [4].
Solvation effects are performed by single point calculations based on the
gas-phase optimized structures using SM5.42R solvation model [5,6] implemented in MN-GSM [7], polarizable continuum model (PCM)
[8,9,10] and a variation of
the conductor-like screening model (COSMO) [11] implemented in GAUSSIAN03 [3].
For additional details, see the following references [12].
Calculation of thermodynamic
quantities
The Thermodynamic quantities are categorized into gas phase and solvation
contributions. The key thermodynamics relations and energy components in the
gas phase are as following:
G = H - TS
H = U + RT
U = E0 + Evib + Erot + Etrans
E0= Eelec + ENN + EZPV = E + EZPV
The definitions of each of these quantities is provided below.
Except for E0 and the energy terms that define it, all the other quantities
above have explicit temperature dependence.
The free energy in solution is the sum of the free energy in gas phase and
the solvation free energy:
Gaq = G + ΔGsol
For additional details, see the following reference [12].
Reference