50
D. Ghosh et al.
fields at the surface of native salmon DNA and the electric fields fluctuate on a 300 fs
time scale with an amplitude of 25 MV/cm due to thermally excited water motions
[70]. Thermal dehybridization of DNA oligomers has been observed using 2D IR
spectroscopy by tracking the four DNA bases independently [71]. Ultrafast 2D IR
study of an RNA double helix in aqueous environment has shown that the equilibrium
sugar-phosphate backbone of RNA and its hydration shell is distinctly different from
hydrated DNA [72]. The 2D IR spectra of RNA display a greater number of backbone
modes than that of DNA, with distinctly different lineshapes of the diagonal peaks
[73].
Quantification of the lipid membrane interior mobility was quantified using N 3 -
alkyl as probe by has illustrated that the spectral diffusion of N 3 -alkyl reflects the
dynamics of the environment, even in the media of very low polarity [74]. Vibrational frequency fluctuations of azide-derivatized amino acids have been investigated
have suggested that the stretching mode of the covalently bonded azide group is
sensitive to the fluctuations of hydrogen bond network system, as found for azide
ions in water [75]. The changes in the secondary structure of the multifunctional
calcium-binding messenger protein Calmodulin (CaM) as a function of temperature and Ca
2+ concentration have been interrogated using 2D IR spectroscopy [76].
Structural dynamics within the distal cavity of wild type heme proteins and several
mutants have shown spectroscopic signatures of interconversion between multiple
protein substates [20, 21, 77, 78]. Complete molecular-level description of proteins
including conformational heterogeneity and their rates of interconversion (has been
studied using picosecond inherent timescale of 2D IR spectroscopy and the high
spatial resolution afforded by the small size of IR chromophores. Ability to introduce the vibrational probe at different specific sights of the protein has allowed
rigorous characterization of dynamics in localized environments and mapping out
the dynamics throughout proteins with atomic spatial resolution and femtosecond
temporal resolution [79–85]. The change in dynamics of an enzyme active sites upon
binding to different inhibitors bound or upon select mutations have been correlated
with the changes in the kinetic isotope effect to understand the role of such motions
play in the enzyme-catalyzed hydrogen transfer reaction [86, 87]. Side-chain structure and dynamics of Histidine as well as ultrafast fluctuations of high amplitude electric fields in lipid membranes have been investigated using 2D IR spectroscopy [88,
89]. The mechanistic aspect of potassium (K) channels, responsible for the selective
permeation of K
+ ions across cell membranes has been studied [90, 91]. The ultrafast
time resolution of 2D IR spectroscopy has provided an instantaneous snapshot of the
multi-ion configurations and structural distributions that occur spontaneously inside
the semisynthetic channel.
2D IR spectroscopy has also been used to investigate materials chemistry. Amide
and carboxylate groups on spherical and aggregated nanoparticles characterized
surface field enhancements, cross peaks, and different line broadening mechanisms
of nanoparticle capping layers [92]. Surface-enhanced two-dimensional infrared (SE
2D IR) vibrational spectroscopy has been used to examine molecules in thin films
of different thicknesses, ranging from a monolayer to ~ 100 nm, including diagonal
and cross peaks measurements [28]. The structural dynamics of planar thin films
D. Ghosh et al.
fields at the surface of native salmon DNA and the electric fields fluctuate on a 300 fs
time scale with an amplitude of 25 MV/cm due to thermally excited water motions
[70]. Thermal dehybridization of DNA oligomers has been observed using 2D IR
spectroscopy by tracking the four DNA bases independently [71]. Ultrafast 2D IR
study of an RNA double helix in aqueous environment has shown that the equilibrium
sugar-phosphate backbone of RNA and its hydration shell is distinctly different from
hydrated DNA [72]. The 2D IR spectra of RNA display a greater number of backbone
modes than that of DNA, with distinctly different lineshapes of the diagonal peaks
[73].
Quantification of the lipid membrane interior mobility was quantified using N 3 -
alkyl as probe by has illustrated that the spectral diffusion of N 3 -alkyl reflects the
dynamics of the environment, even in the media of very low polarity [74]. Vibrational frequency fluctuations of azide-derivatized amino acids have been investigated
have suggested that the stretching mode of the covalently bonded azide group is
sensitive to the fluctuations of hydrogen bond network system, as found for azide
ions in water [75]. The changes in the secondary structure of the multifunctional
calcium-binding messenger protein Calmodulin (CaM) as a function of temperature and Ca
2+ concentration have been interrogated using 2D IR spectroscopy [76].
Structural dynamics within the distal cavity of wild type heme proteins and several
mutants have shown spectroscopic signatures of interconversion between multiple
protein substates [20, 21, 77, 78]. Complete molecular-level description of proteins
including conformational heterogeneity and their rates of interconversion (has been
studied using picosecond inherent timescale of 2D IR spectroscopy and the high
spatial resolution afforded by the small size of IR chromophores. Ability to introduce the vibrational probe at different specific sights of the protein has allowed
rigorous characterization of dynamics in localized environments and mapping out
the dynamics throughout proteins with atomic spatial resolution and femtosecond
temporal resolution [79–85]. The change in dynamics of an enzyme active sites upon
binding to different inhibitors bound or upon select mutations have been correlated
with the changes in the kinetic isotope effect to understand the role of such motions
play in the enzyme-catalyzed hydrogen transfer reaction [86, 87]. Side-chain structure and dynamics of Histidine as well as ultrafast fluctuations of high amplitude electric fields in lipid membranes have been investigated using 2D IR spectroscopy [88,
89]. The mechanistic aspect of potassium (K) channels, responsible for the selective
permeation of K
+ ions across cell membranes has been studied [90, 91]. The ultrafast
time resolution of 2D IR spectroscopy has provided an instantaneous snapshot of the
multi-ion configurations and structural distributions that occur spontaneously inside
the semisynthetic channel.
2D IR spectroscopy has also been used to investigate materials chemistry. Amide
and carboxylate groups on spherical and aggregated nanoparticles characterized
surface field enhancements, cross peaks, and different line broadening mechanisms
of nanoparticle capping layers [92]. Surface-enhanced two-dimensional infrared (SE
2D IR) vibrational spectroscopy has been used to examine molecules in thin films
of different thicknesses, ranging from a monolayer to ~ 100 nm, including diagonal
and cross peaks measurements [28]. The structural dynamics of planar thin films