Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)

Department / School

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.

Library of Congress Subject Headings

Hydrogen bonding.
Amino acids.
Aromatic compounds.


Includes bibliographical references (pages 47-52)



Number of Pages



South Dakota State University



Rights Statement

In Copyright