Disciplines

Computational Chemistry | Physical Chemistry

Abstract (300 words maximum)

The function of biological molecules is closely related to their spatial structure and conformational dynamics. Therefore, understanding the structure and functions of small peptides contributes to gaining insight into the behavior of more complex systems. The peptide bond (-CO-NH-) is among the very important binding patterns in biochemistry. It links amino acids together, specifies rigidity to the protein backbone, and includes the two 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 C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of peptides. In this work, we are testing the computational efficiency and accuracy of various computational methods and basis sets that will be used later to generate potential energy surfaces, dipole moments, and polarizability tensors. We evaluate the energetics and structural parameters of elementary peptide motifs and solvated hydrogen-bonded systems, such as formamide (FA), formamide dimer (FA2), acetamide (AA), N-methyl formamide (NMF), N-methyl acetamide (NMA), isolated NMA and solvated NMA+nH2O. This work is a first step towards the analysis of IR and Raman vibrational spectra of medium and large-size molecules using molecular dynamics simulations, where quantum vibrational methods were computationally demanding due to the high dimensionality of the problem.

Academic department under which the project should be listed

CSM - Chemistry and Biochemistry

Primary Investigator (PI) Name

Martina Kaledin

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Ab initio Calculations of Vibrational Spectra of Model Peptides

The function of biological molecules is closely related to their spatial structure and conformational dynamics. Therefore, understanding the structure and functions of small peptides contributes to gaining insight into the behavior of more complex systems. The peptide bond (-CO-NH-) is among the very important binding patterns in biochemistry. It links amino acids together, specifies rigidity to the protein backbone, and includes the two 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 C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of peptides. In this work, we are testing the computational efficiency and accuracy of various computational methods and basis sets that will be used later to generate potential energy surfaces, dipole moments, and polarizability tensors. We evaluate the energetics and structural parameters of elementary peptide motifs and solvated hydrogen-bonded systems, such as formamide (FA), formamide dimer (FA2), acetamide (AA), N-methyl formamide (NMF), N-methyl acetamide (NMA), isolated NMA and solvated NMA+nH2O. This work is a first step towards the analysis of IR and Raman vibrational spectra of medium and large-size molecules using molecular dynamics simulations, where quantum vibrational methods were computationally demanding due to the high dimensionality of the problem.