heart of biochemistry. This is due to the fact that, the secondary, tertiary and
quaternary structure of a protein involves hydrogen bonds. In addition to this, the
double helical nature of DNA is sustained by the hydrogen bonds between adenine
and thymine; cytosine and guanine. Also, the recognition scheme between an
enzyme and substrate usually involves hydrogen bonding between the active site
and the substrate [1–4].
Under suitable conditions, proton transfer processes can be mediated by
hydrogen bonds and the nature of proton hopping had been a subject of interest.
Significant studies can be seen in a review of DeCoursey [5] and the nature of
intraprotein proton transfer [6] and the recent proton’s active role in Excited State
Intramolecular Proton Transfer (ESIPT) [7].
One of the most conventional methods in studying hydrogen bonding is by
means of infrared spectroscopy. Since 1930s, vibrational signature due to hydrogen
bond has been identified, such observations reveals that there is an associated
bathochromic shift on the stretching frequency of a typical A–H bond when
hydrogen bonding is present [8–10]. However, the study of such systems in condense phase poses some complications, due to the fact that solvation phenomena
can obscure the important peaks of shared proton motion. As a result, gas phase
studies are more favored and do have promising insights.
Experimental studies on the infrared spectra of [NH 3 ] n−1 H
+
, n = 1–5 was pioneered by Schwarz with the interest of obtaining the spectrum of free NH 4
+ and the
effects of hydrogen bonding on it [11]. Unfortunately, the details of the N–N
stretching together with the N–H sp (shared proton) modes were not studied. The
main focus of their study was on the *2,000–4,000 cm
−1 . Later, Lee and
coworkers reported the first observed internal rotation in ionic cluster of
NH 4
+
(NH 3 ) 4 [12]. Furthermore, the same group had proposed that the structure of
NH 4
+ NH 3 has a D 3h geometry, which implies that the shared proton is midway
between the two nitrogen atoms and that it adopts an eclipsed conformation [13].
However, they have speculated that D 3d might be a more stable structure with
approximately 10 cm
−1 lower than the D 3h geometry.
Meanwhile, in terms of the stretching modes of the shared proton, Johnson’s
group performed vibrational predissociation experiments for selected proton bound
symmetric and asymmetric dimers. Based from their results, it was found out that
there is a correlation between the stretching modes of the shared proton with respect
to the differences in the proton affinity, ΔPA of the vicinal Lewis bases [14].
Although stretching modes of the shared proton for symmetric cases were reported;
a correlation between, ΔPA and ν sp is not possible. Moreover, for the case of
symmetric dimers, ν sp depends on the nature of the monomers. This in turn suggests
that aside from proton affinities, there are other factors contributing to ν sp .
Theoretical studies on proton bound ammonia dimer were also reported in the
literature. One of the earliest works was done by Scheiner [15] using HF level of
theory with the minimal basis set; the results had shown that the shared proton is
78
J.A. Tan et al.
quaternary structure of a protein involves hydrogen bonds. In addition to this, the
double helical nature of DNA is sustained by the hydrogen bonds between adenine
and thymine; cytosine and guanine. Also, the recognition scheme between an
enzyme and substrate usually involves hydrogen bonding between the active site
and the substrate [1–4].
Under suitable conditions, proton transfer processes can be mediated by
hydrogen bonds and the nature of proton hopping had been a subject of interest.
Significant studies can be seen in a review of DeCoursey [5] and the nature of
intraprotein proton transfer [6] and the recent proton’s active role in Excited State
Intramolecular Proton Transfer (ESIPT) [7].
One of the most conventional methods in studying hydrogen bonding is by
means of infrared spectroscopy. Since 1930s, vibrational signature due to hydrogen
bond has been identified, such observations reveals that there is an associated
bathochromic shift on the stretching frequency of a typical A–H bond when
hydrogen bonding is present [8–10]. However, the study of such systems in condense phase poses some complications, due to the fact that solvation phenomena
can obscure the important peaks of shared proton motion. As a result, gas phase
studies are more favored and do have promising insights.
Experimental studies on the infrared spectra of [NH 3 ] n−1 H
+
, n = 1–5 was pioneered by Schwarz with the interest of obtaining the spectrum of free NH 4
+ and the
effects of hydrogen bonding on it [11]. Unfortunately, the details of the N–N
stretching together with the N–H sp (shared proton) modes were not studied. The
main focus of their study was on the *2,000–4,000 cm
−1 . Later, Lee and
coworkers reported the first observed internal rotation in ionic cluster of
NH 4
+
(NH 3 ) 4 [12]. Furthermore, the same group had proposed that the structure of
NH 4
+ NH 3 has a D 3h geometry, which implies that the shared proton is midway
between the two nitrogen atoms and that it adopts an eclipsed conformation [13].
However, they have speculated that D 3d might be a more stable structure with
approximately 10 cm
−1 lower than the D 3h geometry.
Meanwhile, in terms of the stretching modes of the shared proton, Johnson’s
group performed vibrational predissociation experiments for selected proton bound
symmetric and asymmetric dimers. Based from their results, it was found out that
there is a correlation between the stretching modes of the shared proton with respect
to the differences in the proton affinity, ΔPA of the vicinal Lewis bases [14].
Although stretching modes of the shared proton for symmetric cases were reported;
a correlation between, ΔPA and ν sp is not possible. Moreover, for the case of
symmetric dimers, ν sp depends on the nature of the monomers. This in turn suggests
that aside from proton affinities, there are other factors contributing to ν sp .
Theoretical studies on proton bound ammonia dimer were also reported in the
literature. One of the earliest works was done by Scheiner [15] using HF level of
theory with the minimal basis set; the results had shown that the shared proton is
78
J.A. Tan et al.