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Updated: Jan 31, 2026

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
Published on: June 27, 2014
Structures and infrared spectroscopy of large sized protonated ammonia clusters
Alhadji Malloum1, Jean Jules Fifen1, Jeanet Conradie2
1Department of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon.
Abstract:
We investigated in this work the structures and relative population of large sized protonated ammonia clusters, , n = 18, 20, 25, 30. To this end, we generated initial geometries using the ABCluster code. The 30 most stable geometries for each of the clusters have been fully optimized at the APFD/6-31++g(d,p) level of theory. The results show that the proton is asymmetrically shared by two ammonia molecules to form the complex. The complex occupies the center of the structures, and it is gradually solvated with increasing cluster size. For n = 25 and n = 30, the first solvation shell of is completely filled with some ammonia molecules present in the second solvation shell. Besides, we have reported the relative population of the investigated clusters at the thermodynamic equilibrium. As a result, the three most stable structures dominate the population of the clusters. For each cluster size, we found that the IR spectra of these three most stable structures are in agreement with experiments. This agreement could be an indication of the reliability of our investigations. Overall, the structures of large sized protonated ammonia clusters are cage-like and exhibit an amorphous behavior.
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