J. C. Dobrowolsk et al.
114
corresponding to symmetric, anti-symmetric and rocking modes of Ch moieties,
were not significantly affected by water, while the C = o band located in the harmonic model above 1650 cm
−1
was sensitive to surrounding water. the authors
concluded that only treating the solvent effects by adding both explicit water molecules and surrounding them by a dielectric media gave a really fair comparison to
experimental vCd spectra [182]. the following paper was devoted to calculations
of the vCd spectra of the alanine zwitterion deuterated at C-atoms and used essentially the same methodology as before [183] (Fig. 5.5).
In the most recent paper by Jalkanen et al. [144] devoted to the theoretical vCd
spectra of L-alanine, dFt Born–oppenheimer molecular dynamics simulations
were performed to determine the locations of the water molecules in the first solvation shell responsible for stabilising the zwitterionic structure [190]. It was found
that as many as 20 water molecules were necessary to fully encapsulate zwitterionic alanine inside a droplet of water, while 11 water molecules were necessary to
encapsulate the polar region of alanine, exposing the hydrophobic methyl group to
the droplet surface, where it migrated during the md simulations. the bulk water
was simulated by different models such as onsager, PCm, and CoSmo. the agreement between experimental and calculated spectra (Fig. 5.5) shows that the use of
explicit water molecules and continuum solvent treatment is very satisfactory for
simulations of L-alanine and, as we shall see further, for other amino acids, even
if the basis set used is not large. the series of studies on L-alanine and related
biological compounds with Jalkanen as a co-author are summarised in Ref. [192].
the problem of a proper computational representation of hydration of the alanine
zwitterion is still a hot issue [144, 190, 191] and it is very likely that the last word
has not been said, yet.
ROA spectra: Experiment and Calculations In the case of the RoA spectra of
L-alanine, early measurements were accompanied by quantum chemical calculations. the first detection of the Raman optical activity (RoA) spectra of L-alanine
in water solutions was performed by hecht et al. in 1989 [193] and Barron et al.
presented the reliable spectra in 1991 [156]. the spectra, recorded in backscattering
mode for the 500–1700 cm
−1
region in neutral, basic and acidic solutions, were
found to be relatively insensitive to ph changes (from 1 N hCl to 1 N Naoh).
however, a broader range of ph (from 6 N hCl to 6 N Naoh) enabled the authors
to observe significant changes in the RoA spectra, to reassign the L-alanine bands
and to refine previous conclusions [194]. It was emphasised that the presence of
RoA structure in regions, where none is seen in the parent Raman spectra, indicate
increased resolution capability. the experimental RoA intensities were compared
with dimensionless circular intensity differences [100] calculated for the L-alanine
zwitterion at the SCF level combined with the 6-31g and 6-31g* basis sets. A
remarkable agreement of the calculated intensities with the experimental parameters in the lower-frequency region was reported.
In 1994, Nafie et al. compared vCd and RoA of L-alanine in water solutions
[179]. A good agreement between the SCF/6-31g* calculated spectra combined with
the onsager self-consistent reaction field and the measured RoA as well as vCd
114
corresponding to symmetric, anti-symmetric and rocking modes of Ch moieties,
were not significantly affected by water, while the C = o band located in the harmonic model above 1650 cm
−1
was sensitive to surrounding water. the authors
concluded that only treating the solvent effects by adding both explicit water molecules and surrounding them by a dielectric media gave a really fair comparison to
experimental vCd spectra [182]. the following paper was devoted to calculations
of the vCd spectra of the alanine zwitterion deuterated at C-atoms and used essentially the same methodology as before [183] (Fig. 5.5).
In the most recent paper by Jalkanen et al. [144] devoted to the theoretical vCd
spectra of L-alanine, dFt Born–oppenheimer molecular dynamics simulations
were performed to determine the locations of the water molecules in the first solvation shell responsible for stabilising the zwitterionic structure [190]. It was found
that as many as 20 water molecules were necessary to fully encapsulate zwitterionic alanine inside a droplet of water, while 11 water molecules were necessary to
encapsulate the polar region of alanine, exposing the hydrophobic methyl group to
the droplet surface, where it migrated during the md simulations. the bulk water
was simulated by different models such as onsager, PCm, and CoSmo. the agreement between experimental and calculated spectra (Fig. 5.5) shows that the use of
explicit water molecules and continuum solvent treatment is very satisfactory for
simulations of L-alanine and, as we shall see further, for other amino acids, even
if the basis set used is not large. the series of studies on L-alanine and related
biological compounds with Jalkanen as a co-author are summarised in Ref. [192].
the problem of a proper computational representation of hydration of the alanine
zwitterion is still a hot issue [144, 190, 191] and it is very likely that the last word
has not been said, yet.
ROA spectra: Experiment and Calculations In the case of the RoA spectra of
L-alanine, early measurements were accompanied by quantum chemical calculations. the first detection of the Raman optical activity (RoA) spectra of L-alanine
in water solutions was performed by hecht et al. in 1989 [193] and Barron et al.
presented the reliable spectra in 1991 [156]. the spectra, recorded in backscattering
mode for the 500–1700 cm
−1
region in neutral, basic and acidic solutions, were
found to be relatively insensitive to ph changes (from 1 N hCl to 1 N Naoh).
however, a broader range of ph (from 6 N hCl to 6 N Naoh) enabled the authors
to observe significant changes in the RoA spectra, to reassign the L-alanine bands
and to refine previous conclusions [194]. It was emphasised that the presence of
RoA structure in regions, where none is seen in the parent Raman spectra, indicate
increased resolution capability. the experimental RoA intensities were compared
with dimensionless circular intensity differences [100] calculated for the L-alanine
zwitterion at the SCF level combined with the 6-31g and 6-31g* basis sets. A
remarkable agreement of the calculated intensities with the experimental parameters in the lower-frequency region was reported.
In 1994, Nafie et al. compared vCd and RoA of L-alanine in water solutions
[179]. A good agreement between the SCF/6-31g* calculated spectra combined with
the onsager self-consistent reaction field and the measured RoA as well as vCd