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Molecular dynamics (MD) simulations of rigid water model TIP4P-EW at ambient conditions were carried out. Delaunay’s simplexes were considered as structural elements of liquid water. Topological criterion which allows to identify the water microstructure in snapshot of MD cell was used to allocate its dense part. Geometrical analysis of water Delaunay’s simplexes indicates their strong flatness in comparison with a regular tetrahedron that is fundamentally different from the results for dense part of simple liquids. The statistics of TIP4P-EW water clusters was investigated depending on their cardinality and connectivity. It is similar to the statistics for simple liquids and the structure of this dense part is also a fractal surface consisting of the free edges of the Delaunay’s simplexes.

Numerical calculations of structures and vibrational spectra of small water clusters are performed by solution of the molecular Schrodinger equation in the density functional theory framework using B3LYP and X3LYP hybrid functionals. Spectral features and evolution of hydrogen bond properties in clusters with their size increasing are discussed. The vibrotational Hamiltonian parameters and Fermi and Darling-Dennison anharmonic resonances in small water oligomers are determined. Obtained results may be used in quantum mechanics/molecular dynamics simulations of water and processes in active site of enzyme.

The paper proposes a set of fairly simple analysis algorithms that can be used to analyze a wide range of protein-protein interactions. In this work, we jointly use the methods of Brownian and molecular dynamics to describe the process of formation of a complex of plastocyanin and cytochrome f proteins in higher plants. In the diffusion-collision complex, two clusters of structures were revealed, the transition between which is possible with the preservation of the position of the center of mass of the molecules and is accompanied only by a rotation of plastocyanin by 134 degrees. The first and second clusters of structures of collisional complexes differ in that in the first cluster with a positively charged region near the small domain of cytochrome f, only the “lower” plastocyanin region contacts, while in the second cluster, both negatively charged regions. The “upper” negatively charged region of plastocyanin in the first cluster is in contact with the amino acid residue of lysine K122. When the final complex is formed, the plastocyanin molecule rotates by 69 degrees around an axis passing through both areas of electrostatic contact. With this rotation, water is displaced from the regions located near the cofactors of the molecules and formed by hydrophobic amino acid residues. This leads to the appearance of hydrophobic contacts, a decrease in the distance between the cofactors to a distance of less than 1.5 nm, and further stabilization of the complex in a position suitable for electron transfer. Characteristics such as contact matrices, rotation axes during the transition between states, and graphs of changes in the number of contacts during the modeling process make it possible to determine the key amino acid residues involved in the formation of the complex and to reveal the physicochemical mechanisms underlying this process.