5 α-Amino Acids In Water: A Review of VCD and ROA Spectra
101
5.4.3 Theoretical Modelling of a Molecule in
Solution in the Context of Optical Spectroscopy
most studies on amino acids have been performed in liquid phase, as it is a natural
environment for bioprocesses. In liquid phase, the problem of the theoretical modeling acquires an additional dimension: the environment. the majority of the vCd and
RoA measurements are taken in solution (in the case of biological species, in aqueous
solution), while few of them are provided in m atrix-isolation or gas-phase environments. until now, there have been no experimental gas-phase or matrix-isolation RoA
spectra of amino acids. therefore, the simulation of solvent effects is of fundamental
importance for a fair comparison between the experimental and theoretical data.
moreover, the conformational changes in the structure as a function of solvent
polarity and ph should be followed. A number of studies have shown that the effect
of the solvent significantly changes the structures, energies and spectra of a system
[65]. Some structures are not stable in the gas phase and gain stability in solvents.
the term “solvation” denotes that the solute molecules m are dissolved in the
liquid phase, the “solvent” S. the solvent is considered an assembly of molecules,
treated as a continuous, homogeneous, isotropic medium, held together by noncovalent interactions and characterised by specific macroscopic properties (density,
dielectric constant, refractive index, etc.). here, a brief overview of the computational methods that are utilised to study solvation phenomena in vCd and RoA
spectroscopy is given. We limit the review to first-principle ab initio calculations,
and concentrate on the most widespread solvation models.
there are three main groups of methods for evaluating the effects of the surrounding solvent on spectroscopic parameters:
1. the supermolecular approach (Sm), i.e. the explicit model, where both the solute
molecule and some neighbouring solvent molecules are explicitly included in the
quantum mechanics (Qm) calculations. the explicit solvent model is especially used to model intermolecular interactions, among them, the formation of a
hydrogen-bonded clusters surrounding the solute molecule.
2. the continuum models, i.e., implicit models, are a family of dielectric polarised
continuum models (PCm), in which the solvent is modelled as a macroscopic
continuum dielectric medium (assumed to be homogeneous and isotropic) characterised by a scalar dielectric constant. the solute, placed in a cavity in a dielectric medium, is described at the Qm level, while the solute-solvent interaction
is described as the mutual polarisation of solute and solvent.
3. Combined molecular dynamics-quantum calculations, md/Qm, is called the
hybrid model. to evaluate the effect of solvation, a classical (md) or quantum
molecular dynamics simulation of the system is performed, and next a number
of configurations of the solute molecule plus some solvent molecules, up to a
given cut-off distance from the solute, is extracted from the trajectory file. It is
then possible to perform a supermolecular calculation (Qm) on the cluster and to
average the results over a given number of configurations to obtain the spectroscopic parameters in liquid phase. In addition, the second solvation shell could
be described by one of the family of PCm models.
101
5.4.3 Theoretical Modelling of a Molecule in
Solution in the Context of Optical Spectroscopy
most studies on amino acids have been performed in liquid phase, as it is a natural
environment for bioprocesses. In liquid phase, the problem of the theoretical modeling acquires an additional dimension: the environment. the majority of the vCd and
RoA measurements are taken in solution (in the case of biological species, in aqueous
solution), while few of them are provided in m atrix-isolation or gas-phase environments. until now, there have been no experimental gas-phase or matrix-isolation RoA
spectra of amino acids. therefore, the simulation of solvent effects is of fundamental
importance for a fair comparison between the experimental and theoretical data.
moreover, the conformational changes in the structure as a function of solvent
polarity and ph should be followed. A number of studies have shown that the effect
of the solvent significantly changes the structures, energies and spectra of a system
[65]. Some structures are not stable in the gas phase and gain stability in solvents.
the term “solvation” denotes that the solute molecules m are dissolved in the
liquid phase, the “solvent” S. the solvent is considered an assembly of molecules,
treated as a continuous, homogeneous, isotropic medium, held together by noncovalent interactions and characterised by specific macroscopic properties (density,
dielectric constant, refractive index, etc.). here, a brief overview of the computational methods that are utilised to study solvation phenomena in vCd and RoA
spectroscopy is given. We limit the review to first-principle ab initio calculations,
and concentrate on the most widespread solvation models.
there are three main groups of methods for evaluating the effects of the surrounding solvent on spectroscopic parameters:
1. the supermolecular approach (Sm), i.e. the explicit model, where both the solute
molecule and some neighbouring solvent molecules are explicitly included in the
quantum mechanics (Qm) calculations. the explicit solvent model is especially used to model intermolecular interactions, among them, the formation of a
hydrogen-bonded clusters surrounding the solute molecule.
2. the continuum models, i.e., implicit models, are a family of dielectric polarised
continuum models (PCm), in which the solvent is modelled as a macroscopic
continuum dielectric medium (assumed to be homogeneous and isotropic) characterised by a scalar dielectric constant. the solute, placed in a cavity in a dielectric medium, is described at the Qm level, while the solute-solvent interaction
is described as the mutual polarisation of solute and solvent.
3. Combined molecular dynamics-quantum calculations, md/Qm, is called the
hybrid model. to evaluate the effect of solvation, a classical (md) or quantum
molecular dynamics simulation of the system is performed, and next a number
of configurations of the solute molecule plus some solvent molecules, up to a
given cut-off distance from the solute, is extracted from the trajectory file. It is
then possible to perform a supermolecular calculation (Qm) on the cluster and to
average the results over a given number of configurations to obtain the spectroscopic parameters in liquid phase. In addition, the second solvation shell could
be described by one of the family of PCm models.