Quantum Mechanical Insights into Biological Processes at the Electronic Level - Computational Modeling of Biological Systems - page 118

MP Møller-Plesset (perturbation theory)

MRCC Multireference coupled cluster

MRCI Multireference configuration interaction

SCF Self consistent field

PES Potential energy surface

PT Perturbation theory

QM/MM Quantum mechanical molecular mechanical

RHF Restricted Hartree-Fock

TD-DFT Time-dependent density functional theory

TISE Time independent Schrodinger equation

UHF Unrestricted Hartree-Fock

ZPE Zero point energy

1 Introduction

The realm of biology is always governed by underlying electronic effects. These
effects are often treated implicitly and may go nearly unnoticed in classical
biomolecular simulations, such as Monte Carlo or molecular dynamics. It is
important to remember, however, that these classical methods always operate on
the single, ground electronic potential energy surface (PES). Furthermore, classical
methods assume the classical behavior of the atomic nuclei, and thus rely on
the so-called Born-Oppenheimer approximation (BAO) heavily used in quantum
mechanics, as discussed in detail below. Due to the BAO, the ground PES can be
obtained by finding the optimal electronic solution for every position of stationary
classical nuclei. The combined electronic and nuclear energy as a function of
nuclear coordinates in the PES. The Born-Oppenheimer PES is usually very
close to the chemical reality. Parameters of classical force fields are optimized to
reproduce this ground PES, either calculated quantum mechanically or derived from
the experiment. Thus, electronic structure is always an active player in classical
simulations through the parameters of the force field in use. However, when it
comes to the assessment of the mechanism of a biochemical reaction that involves
breaking and forming of covalent bonds, quantum mechanics is an almost exclusive
reliable approach, with a prominent classical exception being the empirical valence
bond method. Furthermore, there is a large class of biological processes that simply
cannot be assessed without explicit quantum mechanical treatment. An obvious
example is electron transfer in enzymes or DNA that plays a pivotal role in every
oxidation or reduction event in living cells. Proton or hydrogen transfer is also a
process in which quantum effects are not to be ignored, because these light particles
tunnel through reaction barriers, which are thereby considerably reduced. As an
illustration, it is well-known that the nuclear fusion in the Sun responsible for the
heat that the Sun irradiates would be kinetically impossible without H tunneling.
The Sun is simply not hot enough to overcome the barrier to the H

He
reaction classically. Electronic structure of transition metals is at the heart of the

C H !