idealization, or abstraction related to omitting some of the interactions, when
constructing model structure of material under investigation. The type and range of
simplifications depends heavily on the complexity of the system and hence the next
sections of this chapter will be devoted to this issue described from the viewpoint of
the most frequently used simplifications of structural models, followed in consecutive subchapter by discussion of the simplifications related to the level of theory
employed in calculations (applied formalism, basis functions used to define
molecular or crystal orbitals, type of crystalline potential, termination method used
for smaller structural fragments cut out of a complex structure for their stabilization,
etc.).
1.3.1.1 Size of the System: Molecules, Clusters, Amorphous
and Periodic Solids
The simplest systems, which in many cases do not require any additional model
simplifications, are molecules and charge neutral clusters. Obtained results are
usually in very good agreement with experimental data, especially those obtained in
the gas phase. In the case of molecules in solutions, the situation complicates
significantly, due to additional interactions of those molecules with surrounding
solvent molecules. In such cases, solvation models of varying complexity are
usually used, the broader discussion of which goes beyond the scope of this chapter.
These can be the so-called implicit (continuous), explicit, or hybrid solvation
models. In the implicit solvation models, the solvent interacting with the molecule
under the study is represented as a continuous medium devoid of the properties of
individual “explicit” solvent molecules [117]—the most commonly used implicit
models are polarizable continuum model (PCM) [118, 119] and COnductor-like
Screening MOdel (COSMO) [120, 121]. In contrast, explicit solvation models treat
the solvent molecules explicitly (i.e., in general, their coordinates and interactions
with the molecule studied are explicitly included) [122]. The problem is, however,
that due to the complexity of such explicit solvation approach, its use is usually
limited to classical MM/MD applications and the main effort is put to find appropriate force field allowing accurate and realistic modeling. The third group of
models, hybrid solvation models, is a kind of trade-off, taking the best from both
worlds—the efficiency of implicit solvation models and accuracy of explicit solvation models and usually treats the solvent molecules closest to studied molecule
or cluster explicitly and the remaining part of the solvent implicitly as continuous
uniform solution [123].
A separate group of systems are charged ions and clusters of various sizes, which
require additional treatments related to the overall charge neutralization, because
such charge-possessing systems are computationally unstable and it is usually
impossible to perform calculations related to the structure relaxation and finding the
equilibrium geometry. Typically, the charge neutralization and stabilization of the
structure of the studied system is achieved by adding external, constant charge, or
placing additional cations or anions in the proximity of the ion or cluster (depending
1 Computational Methods in Spectroscopy
33
constructing model structure of material under investigation. The type and range of
simplifications depends heavily on the complexity of the system and hence the next
sections of this chapter will be devoted to this issue described from the viewpoint of
the most frequently used simplifications of structural models, followed in consecutive subchapter by discussion of the simplifications related to the level of theory
employed in calculations (applied formalism, basis functions used to define
molecular or crystal orbitals, type of crystalline potential, termination method used
for smaller structural fragments cut out of a complex structure for their stabilization,
etc.).
1.3.1.1 Size of the System: Molecules, Clusters, Amorphous
and Periodic Solids
The simplest systems, which in many cases do not require any additional model
simplifications, are molecules and charge neutral clusters. Obtained results are
usually in very good agreement with experimental data, especially those obtained in
the gas phase. In the case of molecules in solutions, the situation complicates
significantly, due to additional interactions of those molecules with surrounding
solvent molecules. In such cases, solvation models of varying complexity are
usually used, the broader discussion of which goes beyond the scope of this chapter.
These can be the so-called implicit (continuous), explicit, or hybrid solvation
models. In the implicit solvation models, the solvent interacting with the molecule
under the study is represented as a continuous medium devoid of the properties of
individual “explicit” solvent molecules [117]—the most commonly used implicit
models are polarizable continuum model (PCM) [118, 119] and COnductor-like
Screening MOdel (COSMO) [120, 121]. In contrast, explicit solvation models treat
the solvent molecules explicitly (i.e., in general, their coordinates and interactions
with the molecule studied are explicitly included) [122]. The problem is, however,
that due to the complexity of such explicit solvation approach, its use is usually
limited to classical MM/MD applications and the main effort is put to find appropriate force field allowing accurate and realistic modeling. The third group of
models, hybrid solvation models, is a kind of trade-off, taking the best from both
worlds—the efficiency of implicit solvation models and accuracy of explicit solvation models and usually treats the solvent molecules closest to studied molecule
or cluster explicitly and the remaining part of the solvent implicitly as continuous
uniform solution [123].
A separate group of systems are charged ions and clusters of various sizes, which
require additional treatments related to the overall charge neutralization, because
such charge-possessing systems are computationally unstable and it is usually
impossible to perform calculations related to the structure relaxation and finding the
equilibrium geometry. Typically, the charge neutralization and stabilization of the
structure of the studied system is achieved by adding external, constant charge, or
placing additional cations or anions in the proximity of the ion or cluster (depending
1 Computational Methods in Spectroscopy
33