Question

Please note that this is regarding a Biophysical Chemistry class-college level

Calculate the average lifetime of an ordinary hydrogen bond at room temperature.

Please, I really need help.

Thank you in advance.

Answer 1

To find the average lifetime of an ordinary hydrogen bond at room temperature Molecular Dynamics is used as a biophysical study tool

Analysis of the ordinary hydrogen bond involves average number of H-bonds 〈N_hb〉 formed between the protein and the surrounding water molecules.

〈N_hb〉 = N_hb /  N_step

where N_hb is the total number of H-bonds found

and N_step is the number of trajectory frames.

The average lifetime T_h is

T_h = 〈N_hb〉 * t_run / N_DW

where t_run is the length of simulation runs

and N_DW is the number of water molecules forming H-bonds with amino acid residue during the time t_run.

source :Molecular Dynamics of Water at the Protein-Solvent Interface

Anna Rita Bizzarri* and Salvatore Cannistraro Unita’ INFM, Dipartimento di Scienze Ambientali, UniVersita' della Tuscia, I-01100 Viterbo, Italy