Water bonds electronic structure calculations

Numerous H-bonded homodimers and heterodimers have been investigated using ab initio electronic structure calculations and density functional theory (DFT)-based methods [1-4]. Various aspects of H-bonding starting from classical definition to H-bonded dimers have been discussed in one of the earlier reviews by Kollman and Allen [47]. Water dimer is a typical example used to explain the H-bonding interaction. The structure of the water dimer was analyzed by a molecular beam electric resonance experiment [48, 49]. Almost all theoretical methods developed so far have been employed to predict the... 

It is well known that water-mediated interaction stabilizes structure of biomolecules [1, 138, 247-250]. Therefore, several model molecular systems have been chosen to probe the water-mediated interactions in biomolecules and a large amount of experimental and theoretical work has been published over the years on this subject [78, 138, 251-258]. Since phenol is the simplest aromatic alcohol resembling chromophore of an aromatic amino acid, hydration of phenol molecules has been studied to understand H-bonding and solute-solvent interaction in biological systems. Several experimental and theoretical calculations have been made on the phenol-water clusters [259-273]. Recently, we have made a comprehensive analysis on structure, stability, and H-bonding interaction in phenol (P1-4), water (W1-4), and phenol-water (PmW (w = 1-3, n = 1-3, w + n < 4)) clusters using ab initio and DFT methods [245]. In this section, electronic structure calculations combined with AIM analysis on phenol-water clusters are presented. 

Most of the electronic structure calculations have concentrated on (1) the structure, (2) long-range interaction, (3) peptide-water interaction, and (4) electronic properties. These studies have also affirmed the central role played by the H-bonding interactions in protein. The possibility of the AIM theory to analyze a polypeptide or a particular portion of a peptide has been described [6,323,324]. The existence of H-bond in the peptides has been confirmed by the presence of corresponding bond path in the electron density. Properties associated with the path have also been characterized in terms of p r ) at HBCPs and ring CPs. 

Jensen [3.11] as well as Teeter [3.12] studied by X-ray diffraction the structure of water molecules in the vicinity, at the surface and inside of protein crystals. Jensen used rubredoxin (CEB) crystals to deduce the structure of water from the density distribution of electrons, calculated from diffraction pictures. Jensen found that water molecules which are placed within approx. 60 nm of the protein surface form a net, which is most dense in the distance of a hydrogen bond at the donor- or acceptor- molecules of a protein. In distances larger than 60 nm, the structure of water becomes increasingly blurred, ending in a structureless phase. Water molecules are also in the inside of proteins, but are more strongly bound than... 

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