Abbreviations
CAD
Computer-aided design
DFT
Density functional theory
QM
Quantum mechanics
QM/MM Quantum mechanics/molecular mechanics
RPKA
Reaction progress kinetic analysis
TST
Transition-state theory
1 Introduction
Computer-aided design (CAD) is today an essential tool in fields such as electronics,
architecture, or mechanical and civil engineering. Complex electronic circuits, highperformance aircrafts, high-rise buildings, or sophisticated bridges can be designed
from start to finish, and costly fabrication can be undertaken with the confidence that
the result will meet the features and behaviors predicted by CAD programs.
Synthetic chemistry is a more complex and elusive field. Although electronic
circuits are also assembled with devices (transistors) based on quantum mechanics
(QM) effects, those effects remain internal to each device (that can be seen as a
building brick) and the interaction of devices can be treated with simple and classical
circuit laws. By contrast, in synthetic chemistry, where building blocks are atoms
and molecules, not only the internal behavior but also the interactions between the
different blocks need to be described by their quantum properties. This results in two
special traits: prediction of the results can become a very complex problem, but it
pays off by the richness of features that can be obtained that is incomparably more
varied than those of, for example, a set of electronic devices of similar complexity.
Synthetic chemistry can be regarded as the purposeful execution of a system of
chemical reactions to obtain a product. For a reaction mechanism (Fig. 1 (a) and (b)),
the energy profile (c) determines the kinetic concentration over time (d) that the
reactants will follow, normally through the formation of intermediates, to yield the
desired products and possibly some undesired by-products. Figure 1a, b shows two
equivalent representations of the reaction mechanisms.
Computers can be used in synthetic chemistry for two different roles:
1. Automatization: Control of the instruments to perform the desired processing
tasks
2. Computation: Design and optimization of new synthetic routes
Both roles can be played within two different environments: industry and
research. However, the use of computation is seen from a different perspective in
each environment. For industrial applications, the goal is the precise and targeted
modeling of a specific reaction, and this is often easier to achieve by constructing
82
M. Jaraíz
CAD
Computer-aided design
DFT
Density functional theory
QM
Quantum mechanics
QM/MM Quantum mechanics/molecular mechanics
RPKA
Reaction progress kinetic analysis
TST
Transition-state theory
1 Introduction
Computer-aided design (CAD) is today an essential tool in fields such as electronics,
architecture, or mechanical and civil engineering. Complex electronic circuits, highperformance aircrafts, high-rise buildings, or sophisticated bridges can be designed
from start to finish, and costly fabrication can be undertaken with the confidence that
the result will meet the features and behaviors predicted by CAD programs.
Synthetic chemistry is a more complex and elusive field. Although electronic
circuits are also assembled with devices (transistors) based on quantum mechanics
(QM) effects, those effects remain internal to each device (that can be seen as a
building brick) and the interaction of devices can be treated with simple and classical
circuit laws. By contrast, in synthetic chemistry, where building blocks are atoms
and molecules, not only the internal behavior but also the interactions between the
different blocks need to be described by their quantum properties. This results in two
special traits: prediction of the results can become a very complex problem, but it
pays off by the richness of features that can be obtained that is incomparably more
varied than those of, for example, a set of electronic devices of similar complexity.
Synthetic chemistry can be regarded as the purposeful execution of a system of
chemical reactions to obtain a product. For a reaction mechanism (Fig. 1 (a) and (b)),
the energy profile (c) determines the kinetic concentration over time (d) that the
reactants will follow, normally through the formation of intermediates, to yield the
desired products and possibly some undesired by-products. Figure 1a, b shows two
equivalent representations of the reaction mechanisms.
Computers can be used in synthetic chemistry for two different roles:
1. Automatization: Control of the instruments to perform the desired processing
tasks
2. Computation: Design and optimization of new synthetic routes
Both roles can be played within two different environments: industry and
research. However, the use of computation is seen from a different perspective in
each environment. For industrial applications, the goal is the precise and targeted
modeling of a specific reaction, and this is often easier to achieve by constructing
82
M. Jaraíz