Chemistry Reference
In-Depth Information
first part the review summarizes investigations on the reliability of pure theoretical
approaches to ED and its Laplacians.
Keywords Electron density
Ab initio
QM/MM
Environmental effects
Source
function
E64c
Cathepsin B
AMCHA
Basis set effects
Contents
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
2 The Accuracy of Theoretical and Experimental Electron Densities . . . . . . . . . . . . . . . . . . . . . . . 52
3 Environmental Effects on EDs of Biologically Active Molecules . . . . . . . . . . . . . . . . . . . . . . . . . 61
4 On the Applicability of the Source Function in QM/MM Investigations . . . . . . . . . . . . . . . . . . 83
5 Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
1
Introduction
Dalton's atomic hypothesis together with the work of van't Hoff and Le Bel formed
the basics to the modern view of matter within which a chemical bonding network
links atoms to molecules, aggregates, liquids, or the solid state. This concept is the
most widely applied and fundamental model in chemistry and forms, e.g., the basis
of the Lewis notation, which provides a reasonable and generally accepted expla-
nation for the electronic and geometric structures of almost all molecules. However,
since the 1920s we know that chemical bonding can only be properly understood as
a quantum mechanical phenomenon. Furthermore, the work of Kohn and coworkers
[
1
,
2
] proved that in principle the electron density (ED) determines all physical and
chemical properties of a given molecule [
3
-
6
]. The ED is also the underlying
quantity in density functional theory (DFT) [
7
,
8
] and readily available from
wave-function-based approaches. Its interpretation in terms of bonding effects is
possible for example by the quantum theory of atoms in molecules (QTAIM) [
9
,
10
]. This approach allows to quantify the nature of chemical interactions and
provides a solid quantum mechanical methodology which allows to interpret the
ED. Nevertheless, due to the inherent ambiguity of any interpretation of quantum
mechanical properties in terms of localized atomic quantities, QTAIM does not
provide an unique interpretation of chemical bonding. Hence, alternatives such as
valence bond-based methods [
11
], energy partitioning approaches [
12
], population
analyses [
13
,
14
], and many others are also important tools.
The ED represents a physical observable as was first noticed by Debye [
15
].
However, as nicely highlighted in a recent article of Coppens [
16
], it took much
effort to develop an experimental machinery which allows to measure this property
with the required accuracy and efficiency. Due to simultaneous developments in
experimental setups and analyzing software tools [
10
], EDs of entire compound
classes [
17
-
20
] or proteins are today available [
19
,
21
-
29
], and even more, the
routine application of ED measurements is in sight. However, from the literature it
