Search

Prussian Blue (PB) or ferric hexacyanoferrate (II) is one of the most attractive materials in green battery industry. It has defective structure (d-PB), Fe 4 III [ Fe II ( CN ) 6 ] 3 ⋅ xH 2 O ( x ≈ 14 − 16 ) , that one of [Fe(CN)6]4− group is missing, and hydrated with water molecules at the 24e empty nitrogen site. In this study, we investigated the distributions of water and Li+ in d-PB by using three-dimensional reference interaction site-model (3D-RISM) theory, which is a statistical mechanics theory of molecular liquids. The theory can examine the selective ion adsorption in solvated molecular materials. The results from 3D-RISM show that there are 14 water molecules located in different positions inside the d-PB lattice, which are in good agreement with experiment. Moreover, we also found the Li+ distributed at inside d-PB lattice positioned closely to the 32f spherical cavity of d-PB.

Molecular recognition (MR) is an essential elementary process allowing biomolecules to perform their function. MR can be defined as a molecular process in which one or several guest molecules are bound with a high probability at a particular site such as a cleft or a cavity, of a host molecule in a particular orientation. It is a thermodynamic process which is characterised by the difference of the free energies between two states of a host–guest system, bound and unbound. The process features an extremely heterogeneous atomic-environment around binding sites, which has turned away challenges by the conventional statistical mechanics of liquids, e.g. a mean field theory. We have been developing a new theory for MR in biomolecular systems, based on the statistical mechanics of liquids, or the 3D-reference interaction site model (RISM)/RISM theory. The theory has demonstrated its amazing capability of predicting the process from the first principle. In this article, we review our recent works on MR concerni...

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the 3D-RISM/RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as “recognized” by the protein. 3D-distribution functions can be obtained by means of 3D-RISM/RISM theory. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands such as water, ions, and carbon monoxide by a protein.

The equilibrium distribution function of water in the aquaporin-Z is calculated based on the three-dimensional reference interaction site model theory. It is found that water in aquaporin-Z distributes continuously throughout the channel with the open structure, while the distribution has a conspicuous gap around the R189 side chain in the closed form. The gating mechanism of the channel is inferred from the water distribution. The method also provides information with respect to the distribution of hydrogen atoms of water inside the channel, which is important to investigate the conduction mechanism of molecules including protons in the channel.

“Molecular recognition” is one of the most important molecular processes for living systems in order to maintain their life, since most of the biological functions are initiated with the process. Understanding of the process is also important for designing a new drug. Firstly, it is important to find a target of a drug, which is in many cases a function of protein or DNA to be inhibited. Secondly, binding a drug molecule to the active site of a biomolecule itself is a “molecular recognition process. In the present article, we review our recent studies on the molecular recognition process, carried out by means of the 3D-RISM theory, a statistical mechanics theory of liquids. Studies on the conduction mechanisms in two types of molecular channels, aquaporin and the M2 channels, are reviewed.

Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.

Cations (Ca2+, Na+, K+) selectively bound by human lysozyme and its mutants are probed by the 3D-RISM theory, a statistical mechanics theory of liquids.

Water and hydronium ion distribution inside aquaporin channels are probed by the 3D-RISM theory, a statistical mechanics theory of liquids.