68
P. Panwaria and A. Das
grid, as well as the extraction grid and the accelerating grid, is 1 cm. The ions are
finally detected by a dual chevron type microchannel plate (MCP) detector placed
at the end of the TOF tube. The detector is housed in a small chamber pumped by
a turbomolecular pump (speed ~ 70 lit/s), and the operating pressure is maintained
at ~ 2 × 10
–7 mbar. The detector voltage is set at ~ -2800 V. A grounding mesh is
placed just before the detector to ensure that the ions coming out of the accelerating
grid travel the field-free region of the TOF tube with the same kinetic energy. The
ions with different masses reach the detector at different times, and thus the time of
flight of the ions can be converted into their masses. The ion signal from the detector
is further amplified using a preamplifier and fed into a digital oscilloscope. The TOF
mass spectrum of the molecule or complex is recorded at a single wavelength of
the UV laser, and the mass-selected electronic spectrum is obtained by selecting
a particular mass channel on the oscilloscope trace and tuning the wavelength of
the laser. Data acquisition from the oscilloscope and simultaneous scanning of the
laser wavelength is done through a USB interface using LabView based programs.
In the case of the UV-UV and IR-UV double resonance spectroscopy techniques,
synchronization of the timing sequence of the lasers is controlled by the digital delay
generator.
In the case of the LIF spectroscopy, the UV/IR laser beam intersects the molecular
beam in the perpendicular direction at a distance of ~1 cm from the orifice of the pulse
valve. Fluorescence is collected from the intersection point in the direction mutually
orthogonal to the direction of the molecular beam and the laser beam through a lens to
the photomultiplier tube (PMT) [158, 159]. The signal from the PMT is transferred to
a digital oscilloscope, and the LIF spectra are acquired in a computer through a USB
interface using Labview based programs. The results, which will be discussed in this
chapter, are mostly derived from the mass analyzed REMPI spectroscopy technique
while the samples are vaporized by thermal heating. The experimental results are
analyzed with the help of quantum chemistry calculations performed using Gaussian
09 [160], Q-Chem [161], NBO [162], and Gamess-USA [163] software packages.
3 Results and Discussion
3.1 Interplay Between Multiple Non-Covalent Interactions
The fine interplay between multiple non-covalent interactions dictates most of the
structures of biomolecules and materials. A few best examples of the molecular
systems having such interplay are DNA, proteins, etc. [1, 4, 164, 165]. A delicate
balance between base-pairing through strong (conventional) hydrogen bonds and
base stacking provides a very distinct double-helical structure of the DNA. Similarly, a subtle co-operation between the strong hydrogen bonding interactions in the
backbone and various other non-covalent interactions between backbone-sidechain
and sidechain-sidechain of proteins renders the folding motifs of their particular
P. Panwaria and A. Das
grid, as well as the extraction grid and the accelerating grid, is 1 cm. The ions are
finally detected by a dual chevron type microchannel plate (MCP) detector placed
at the end of the TOF tube. The detector is housed in a small chamber pumped by
a turbomolecular pump (speed ~ 70 lit/s), and the operating pressure is maintained
at ~ 2 × 10
–7 mbar. The detector voltage is set at ~ -2800 V. A grounding mesh is
placed just before the detector to ensure that the ions coming out of the accelerating
grid travel the field-free region of the TOF tube with the same kinetic energy. The
ions with different masses reach the detector at different times, and thus the time of
flight of the ions can be converted into their masses. The ion signal from the detector
is further amplified using a preamplifier and fed into a digital oscilloscope. The TOF
mass spectrum of the molecule or complex is recorded at a single wavelength of
the UV laser, and the mass-selected electronic spectrum is obtained by selecting
a particular mass channel on the oscilloscope trace and tuning the wavelength of
the laser. Data acquisition from the oscilloscope and simultaneous scanning of the
laser wavelength is done through a USB interface using LabView based programs.
In the case of the UV-UV and IR-UV double resonance spectroscopy techniques,
synchronization of the timing sequence of the lasers is controlled by the digital delay
generator.
In the case of the LIF spectroscopy, the UV/IR laser beam intersects the molecular
beam in the perpendicular direction at a distance of ~1 cm from the orifice of the pulse
valve. Fluorescence is collected from the intersection point in the direction mutually
orthogonal to the direction of the molecular beam and the laser beam through a lens to
the photomultiplier tube (PMT) [158, 159]. The signal from the PMT is transferred to
a digital oscilloscope, and the LIF spectra are acquired in a computer through a USB
interface using Labview based programs. The results, which will be discussed in this
chapter, are mostly derived from the mass analyzed REMPI spectroscopy technique
while the samples are vaporized by thermal heating. The experimental results are
analyzed with the help of quantum chemistry calculations performed using Gaussian
09 [160], Q-Chem [161], NBO [162], and Gamess-USA [163] software packages.
3 Results and Discussion
3.1 Interplay Between Multiple Non-Covalent Interactions
The fine interplay between multiple non-covalent interactions dictates most of the
structures of biomolecules and materials. A few best examples of the molecular
systems having such interplay are DNA, proteins, etc. [1, 4, 164, 165]. A delicate
balance between base-pairing through strong (conventional) hydrogen bonds and
base stacking provides a very distinct double-helical structure of the DNA. Similarly, a subtle co-operation between the strong hydrogen bonding interactions in the
backbone and various other non-covalent interactions between backbone-sidechain
and sidechain-sidechain of proteins renders the folding motifs of their particular