Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Chemistry and Biochemistry

First Advisor

Suvobrata Chakravarty


amino acids, aromatic protons, bonds geometry, chemistry, hydrogen bonds, R and Perl


Hydrogen bonds play critical role in folding, structure and recognition of biological macromolecules (e.g., proteins, RNA, DNA). In addition to classical hydrogen bonds (e.g., ─OH---O=, ─OH---O─, ─NH---O─ etc.), structural analysis of protein and nucleic acids, almost a decade ago, showed that hydrogen bonds (e.g., CH---O) with hydrogen atoms on aliphatic carbon atoms (hereafter, aliphatic-protons) also play very important role in the structure and function of biomolecules. Even though, protons of aromatic ring systems (hereafter, aromatic-protons) are more polar than the aliphatic-protons, systematic analysis of hydrogen bonds of aromatic-protons have not been carried out. Therefore, I carried out a systematic analysis of hydrogen bonds that are made with aromatic-protons of tryptophan, tyrosine and phenylalanine amino acids in high-resolution structures of proteins and their complexes using a computer program that I created in R- and Perl languages. The analysis showed that aromatic CH---O are very common in proteins and tryptophan-CD1 is the most frequent participant in aromatic CH---O hydrogen bonds. The normalized frequency of occurrences of aromatic CH---O hydrogen bonds are greater than that of the aliphatic CH---O hydrogen bonds. Therefore, like aliphatic CH---O hydrogen bonds we anticipate that aromatic CH---O hydrogen bonds are likely to play equally, if not more, important role in macromolecular folding, stability and recognition. The numerous examples of aromatic CH---O hydrogen bonds observed here provides a good source of information that can be probed further by experiments to validate their important contribution.


Includes bibliographical references (pages 47-52)



Number of Pages



South Dakota State University


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