Disciplines
Computational Chemistry | Numerical Analysis and Scientific Computing | Physical Chemistry
Abstract (300 words maximum)
Formamide is a small model compound for the study of the peptide bond. The peptide bond links amino acids together, specifies rigidity to the protein backbone, and includes the essential docking sites for hydrogen-bond-mediated protein folding and protein aggregation, namely, the C=O acceptor and the N-H donor parts. Therefore, the infrared C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of peptides. This computational chemistry work, we study hydrogen bonds in formamide dimer isomers. We evaluate the accuracy of the density functional theory (DFT) and many-body perturbation theory to the 2nd order (MP2) methods in the prediction of structural parameters and vibrational frequencies of formamide and formamide dimer. Also, we assess the importance of basis set superposition error when evaluating binding energy of formamide dimer isomers. This project introduces undergraduate students to methods and tools of computational chemistry.
Academic department under which the project should be listed
Chemistry and Biochemistry
Primary Investigator (PI) Name
Martina Kaledin
Included in
Computational Chemistry Commons, Numerical Analysis and Scientific Computing Commons, Physical Chemistry Commons
Hydrogen bonding in small model peptides; The DFT and MP2 study
Formamide is a small model compound for the study of the peptide bond. The peptide bond links amino acids together, specifies rigidity to the protein backbone, and includes the essential docking sites for hydrogen-bond-mediated protein folding and protein aggregation, namely, the C=O acceptor and the N-H donor parts. Therefore, the infrared C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of peptides. This computational chemistry work, we study hydrogen bonds in formamide dimer isomers. We evaluate the accuracy of the density functional theory (DFT) and many-body perturbation theory to the 2nd order (MP2) methods in the prediction of structural parameters and vibrational frequencies of formamide and formamide dimer. Also, we assess the importance of basis set superposition error when evaluating binding energy of formamide dimer isomers. This project introduces undergraduate students to methods and tools of computational chemistry.