Regulation Effect Of Water Molecules On Structures And Properties Of Protonated Glycine-Praline Dimers

We optimized four groups of protonated amino-acid dimers with respective neutral and zwitterionic structures by attaching various numbers of water molecules at the B3LYP/6-311++G**//6-31+G*level using Gaussian03 software. The four groups of complexes were 1. protonated glycine and glycine dimers (GGH-cs, GGH-zw), 2. protonated proline and proline dimers (PPH-cs,PPH-zw), 3. glycine and protonated proline dimers (GPH-cs, GPH-zw), and 4. proline and protonated glycine dimers (PGH-cs, PGH-zw), respectively; where postfixs cs and zw denote the neutral and zwitterionic dimers respectively. We can obtain different complexes according to the combination of water molecules in different locations. It is clear that water molecules have stronger regulation effect on glycine-proline dimer molecules by comparing the structural parameters, the relative stability of these complexes and activation energy required for intermolecular proton transfer from neutral structure to zwitterionic one.There are six sites which can be combined with water molecules for the protonated glycine dimer (GGH) and they are H1, H2,…, H6, respectively. Stability order of only those complexes with hydration at the sites of H1, H3, or H4 (right glycine species of the GGH dimer) is consistent with that without water molecule combined. Results show that all those cs conformations are more stable than the zw ones. When combined with water molecules at the H2, H5, or H6 sites (left glycine species of GGH dimer), zw complexes will become more stable than the cs ones, indicating the favorable hydration effect of the zw conformations. Parameters of such complexes with water molecules attached have certain regularity.Activation energy required for the transformation from GGH-cs complexes to the GGH-zw ones is minimum when water molecules are bound to the H5 and H6 sites. Activation energy are 8.0 kJ/mol,5.7 kJ/mol,0.4 kJ/mol, respectively when 1 to 3 molecules of water is combined at the H5 or H6 sites. When protonated glycine dimer combine with four molecules of water, these four water molecules all combine to the sites of H5 and H6. H2 proton of the cs glycine transfers to its nitrogen atom spontaneously to form zw complex without extra activation energy required. When water molecules combine to the right of glycine, the intramolecular proton transfer process is difficult to happen. This shows that it play an important regulatory role for the structure of glycine dimer, direction of intermolecular proton transfer and relative stability of these complexes with with different hydrated sites and numbers.There are four binding sites when protonated proline dimer combines water molecules, and they are H1, H2,…, H4, respectively. It will be affected for the transformation from neutral structures to zwitterionic ones in structure, relative stability and activation energy according to combining regulation of water molecules.Different from the stability order of glycine dimers, zw configuration complexes are more stable than cs configuration for all proline dimer complexes. For the activation energy of the process of transformation PPH-cs→PPH-zw, it is least only when water molecules bind to the H4 site. When two water molecules bind to the same position H4, activation energy of proton (H2) transfer is only 0.8 kJ/mol. When three water molecules bind to the site H4 of the neutral complex, spontaneous proton transfer occurs (i.e., without energy barrier). Water molecules can also play an important regulatory role in structure of the proline dimer, the direction of intermolecular proton transfer and relative stability.There are five available binding sites (H1~H5) when protonated glycine-proline dimer and protonated proline-glycine dimer combine water molecules, respectively. GPH-zw dimer conformation is more stable than GPH-cs one and neutral PGH-cs dimer is more stable than GPH-zw one. Activation energy for the transformation from PGH-cs to GPH-zw is 6.0 kJ/mol. Relative stability and activation energy of dimers in such transformation will change a lot because the positions between glycine and proline are different. Both H4 and H5 sites are needed to bind five water molecules for the glycine-proline dimer, but it only needs to bind three water molecules in H5 position for proline-glycine dimer to obtain the more stable zw complex. It indicates that different amino acid has a great influence on the proton transfer process of the whole dimer.