Hydrogen bond energetics:: A simulation and statistical analysis of N-methyl acetamide (NMA), water, and human lysozyme

Energy minimization and molecular dynamics simulations have been used to study hydrogen bond interactions in dimers of N-methylacetamide (NMA), in NMA-water complexes, and in human lysozyme. The potential energy surface is found to be determined by the interactions of entire peptide groups (O=Ci-1-N-i-H) or water molecules rather than by single donor and acceptor groups. The contact distance between the donor hydrogen and the acceptor as well as the angle of the bond at the donor hydrogen are the principal geometric parameters that describe the hydrogen bond. Potential energy surfaces were also examined in the presence and absence of explicit solvent molecules. The results suggest that both competing hydrogen bond interactions and the thermal motion of atoms broaden the distribution of low energy donor-acceptor contacts. Comparisons are made with a statistical analysis of mainchain hydrogen bond donor and acceptor contacts in high-resolution crystal structures of nonhomologous proteins. Interaction energies and geometries of the NMA model system mimic those found in folded polypeptide chains. All systems are characterized by a minimum in the population of donor-acceptor contacts at interaction distances of 2.4-2.6 Angstrom. This minimum originates from spatial constraints that are enhanced by electrostatic interactions in environments that are characterized by competition for hydrogen bonding interactions. The presence of such a minimum in the distribution of donor-acceptor contacts supports the definition of hydrogen bonds by geometrical cutoff criteria with a donor-hydrogen acceptor distance of less than 2.5 Angstrom and an angle of deviation not more than 90 degrees from linearity of the donor, donor-hydrogen and acceptor atoms.