Much earlier even, 2D IR has been applied to investigate structural properties of
DNA by the resolution of inter- and intra-strand coupling between bases [79, 98]. In
other examples, Tokmakoff’s group has extensively investigated the secondary
structure of globular proteins by use of 2D IR [87]. The group has built a whole
library of 16 proteins and assigned fractions of residues to alpha helices, beta sheets
and random structures by help of a singular-value-decomposition analysis of 2D IR
data. That way, a remarkable agreement between 2D IR data and crystal structure
information could be proven. Moreover, the same group also investigated the
dissociation of insulin dimers and unfolding with 2D IR [99]. They used the
observed changes in the spectra to obtain binding constants and to parametrize a full
thermodynamic model for dimerization.
Biomolecular structure and its relation to different types of diseases is a
particularly active field of 2D IR research. Starting from the demonstrations over the
last couple of years, it will be interesting to see if 2D IR has the potential to be
ultimately established as an analytical tool for life sciences. A dream would for
instance be to construct a 2D IR spectrometer, which yields structural information
from biological tissues or could even be applied to in vivo investigations.
The results regarding structural properties of bio-molecular samples that have
been presented in these sections are based mostly on quasi-static 2D IR spectra,
from which structural interpretations have been deduced from observations of either
spectral positions, vibrational couplings, or slow dynamical evolutions thereof.
However, 2D IR has the important advantage to yield structural information from an
ultrafast timescales as fast as picoseconds and below. To illustrate how this is
exploited for molecular structure determination, the following sections will
concentrate on changes in 2D IR spectra that occur between successively delayed
pump and probe pulses during the vibrational lifetime of a particular IR label.
3.1.3 Structural Dynamics Resolved from Spectral Diffusion in 2D IR Spectroscopy
To start with, consider the example of spectral diffusion (Sect. 2), which yields
information on interconversion of the frequencies of oscillators under the envelope
of a broadened vibrational transition. 2D IR spectroscopy is an ideal method for
investigating such dynamics since spectral diffusion can be easily extracted from 2D
IR spectra. Therefore, the method can provide unique insight into the molecular
origin of what is frequently termed ‘‘dynamic heterogeneity’’. Various methods for
data analysis have been developed such as the central line slope method, the nodal
slope or peak ellipticity, all of which can be applied to study spectral diffusion
[69, 70, 100]. Such methods have been tested even in the case of non-Gaussian
dynamics [101]. In addition, theoretical approaches such as structure optimization
on the DFT level or molecular dynamics simulations can be used to directly
compare the experimental results to theoretical predictions and, therefore, lead to an
understanding of the molecular origin of the encountered dynamics
[77, 84, 102, 103]. Consequently spectral diffusion has been extensively used by
many groups to study dynamic structure and environmental interactions in various
samples.
Top Curr Chem (Z) (2017) 375:86
123
134
Reprinted from the journal
DNA by the resolution of inter- and intra-strand coupling between bases [79, 98]. In
other examples, Tokmakoff’s group has extensively investigated the secondary
structure of globular proteins by use of 2D IR [87]. The group has built a whole
library of 16 proteins and assigned fractions of residues to alpha helices, beta sheets
and random structures by help of a singular-value-decomposition analysis of 2D IR
data. That way, a remarkable agreement between 2D IR data and crystal structure
information could be proven. Moreover, the same group also investigated the
dissociation of insulin dimers and unfolding with 2D IR [99]. They used the
observed changes in the spectra to obtain binding constants and to parametrize a full
thermodynamic model for dimerization.
Biomolecular structure and its relation to different types of diseases is a
particularly active field of 2D IR research. Starting from the demonstrations over the
last couple of years, it will be interesting to see if 2D IR has the potential to be
ultimately established as an analytical tool for life sciences. A dream would for
instance be to construct a 2D IR spectrometer, which yields structural information
from biological tissues or could even be applied to in vivo investigations.
The results regarding structural properties of bio-molecular samples that have
been presented in these sections are based mostly on quasi-static 2D IR spectra,
from which structural interpretations have been deduced from observations of either
spectral positions, vibrational couplings, or slow dynamical evolutions thereof.
However, 2D IR has the important advantage to yield structural information from an
ultrafast timescales as fast as picoseconds and below. To illustrate how this is
exploited for molecular structure determination, the following sections will
concentrate on changes in 2D IR spectra that occur between successively delayed
pump and probe pulses during the vibrational lifetime of a particular IR label.
3.1.3 Structural Dynamics Resolved from Spectral Diffusion in 2D IR Spectroscopy
To start with, consider the example of spectral diffusion (Sect. 2), which yields
information on interconversion of the frequencies of oscillators under the envelope
of a broadened vibrational transition. 2D IR spectroscopy is an ideal method for
investigating such dynamics since spectral diffusion can be easily extracted from 2D
IR spectra. Therefore, the method can provide unique insight into the molecular
origin of what is frequently termed ‘‘dynamic heterogeneity’’. Various methods for
data analysis have been developed such as the central line slope method, the nodal
slope or peak ellipticity, all of which can be applied to study spectral diffusion
[69, 70, 100]. Such methods have been tested even in the case of non-Gaussian
dynamics [101]. In addition, theoretical approaches such as structure optimization
on the DFT level or molecular dynamics simulations can be used to directly
compare the experimental results to theoretical predictions and, therefore, lead to an
understanding of the molecular origin of the encountered dynamics
[77, 84, 102, 103]. Consequently spectral diffusion has been extensively used by
many groups to study dynamic structure and environmental interactions in various
samples.
Top Curr Chem (Z) (2017) 375:86
123
134
Reprinted from the journal