Methylviologen dication is easily reduced to a monocation radical, and turned to be blue, forming a charge-transfer complex with a donor molecule. Yoshikawa et al. recently reported photo-induced reduction and charge transfer complexes in polycyano–polycadmate host clathrates. We study this reduction using quantum chemical calculations. The energy changes with the torsion angle of the two catio...

We focus on molecular cavities which are represented in the form of Solvent Excluded Surfaces. They are featured by having smooth toroidal and spherical surface blendings between the constituting atoms. The only inputs are the nuclear coordinates, the van der Waals radii and the probe radius. From those information, our purpose is to generate a patch representation of the resulting Connolly sur...

Structural features of small amino acid sequences are known to determine the dynamic properties and functional specificity of proteins and polypeptides. In this study, the effects of solvation and identity of the varying C-terminal residue on the energetics, structural features of the peptide planes, values of the ψ and ф dihedrals, geometry around the α-carbon atoms and theoretically predicted...

A combined approach to study reactions in solution in which the solute and a number of solvent molecules are described with a hybrid quantum mechanical/molecular mechanical ~QM/MM! method, and the bulk solvent is represented by a polarizable continuum model ~PCM! has been implemented. In this way, both short-range effects of the first-solvation shell and long-range electrostatics due to the bul...

The present mini-review aims first at an introduction to two thermodynamic essentials of the binding between the influenza A virus hemagglutinin (HA) and the cell surface receptor sialoside, (1) the equilibrium 1:1 binding of the HA with the sialoside, (2) the polyvalent effect of the HA binding to the polyvalent sialoside. Second, the review introduces the fragment molecular orbital (FMO) stud...

Oxindole derivatives which are commercially available have got antiviral, antifungal, antibacterial, anticancer, anti-inflammatory, antihypertensive, and anticonvulsant activities. The solvation analysis of oxindole derivatives has been carried out using B3LYP procedure with 6-311++G basis set using ten solvents to compute the electrostatic interaction, repulsive, dispersive energy and cavitati...

We present an extension of the Polarizable Continuum Model (PCM) to the calculation of solvent effects on indirect spin–spin coupling constants for Hartree– Fock wave functions and Density Functional Theory. This is achieved by implementing the PCM model for singlet and triplet linear response functions. The new code is used for calculating the solvent effects on the indirect spin–spin coupling...

Geometry optimizations of all cluster models were carried out in solution with Integral Equation Formalism Polarizable Continuum Model (IEFPCM) as implemented in Gaussian09. The B3LYP functional in conjunction with the 6-31+g(d) basis set was employed to optimize the geometries. Frequency calculations at the same level of theory were carried out to verify the nature of the stationary points enc...

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6-31G* level) is used to opti...