Thermodynamics of van der Waals and Hydrophobic Interactions

Rudolf Zahradnik and Pavel Hobza

Abbreviations

AO Atomic orbital

AMBER Empirical force field

AMI Semiempirical method of quantum chemistry

BSSE Basis set superposition error

CC Coupled-cluster method for calculation of correlation energy

CFF91 Empirical force field

CHARMM Empirical force field

CI Configuration interaction method

CVFF Empirical force field

DISCOVER Program code

DFT Density Functional Theory

DZ Double zeta

Ecor Correlation energy

ESCF Self Consistent Field energy

GROMOS Program code

HF Hartree-Fock quantum chemical method

HFR Hartree-Fock-Roothaan quantum chemical method

LCAO Linear combination of atomic orbitals

MC Monte Carlo method

MD Molecular dynamics method

MM2 Empirical force field

MM3 Empirical force field

MP M0ller-Plesset method for calculation of correlation energy

P.E.S. Potential energy surface

PM3 Semiempirical method of quantum chemistry

QZ Quadruple zeta

SCF Self Consistent Field method

TZ Triple zeta vdW van der Waals (e.g., forces, interactions)

ZPE Zero-point energy

Symbols

a

Constant

dX - dy,dz

Cartesian displacement coordinates

k

Boltzmann constant, parameter

m

Mass

r

Distance

£

Energy

V

Vibration frequency

A

Helmholtz energy

C

Parameter

c c

Heat capacity at constant volume and pressure

De

Dissociation energy

E

Energy

F

Force, matrix of potential energy

G

Gibbs free energy, matrix of kinetic energy

H

Enthalpy, Hamiltonian

I

Moment of inertia

K

Thermodynamic equilibrium constant

M

Power constant

N

Number of particles, power constant

P

Pressure

Q

Partition function

R

Distance, gas constant

S

Entropy, overlap matrix

T

Absolute temperature (in K)

U

Internal energy

V

Volume, potential energy

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