Partial atomic charges describe the distribution of electron density in a molecule, and therefore they provide clues regarding the chemical behaviour of molecules. Atomic charges are frequently used in molecular modelling applications such as molecular dynamics, docking, conformational searches, binding site prediction, etc. Recently, partial atomic charges have also become popular chemoinforma...

We present a de novo design program called SYNOPSIS, that includes a synthesis route for each generated molecule. SYNOPSIS designs novel molecules by starting from a database of available molecules and simulating organic synthesis steps. This way of generating molecules imposes synthetic accessibility on the molecules. In addition to a starting database, a fitness function is needed that calcul...

The first principles were calculated to study the adsorption behaviors of caffeine molecules on the pristineand N-doped TiO2 anatase nanoparticles. Both oxygen and nitrogen in the caffeine molecule can reactstrongly with TiO2 nanoparticle. Thus, the binding sites were located on the oxygen or nitrogen atom ofthe caffeine, while the binding site of the TiO2 nanoparticle occurs ...

The motion of water molecules in a gramicidin-like channel was studied by the molecular dynamics method. Water molecules are presented in the ST2 model. The structure of the channel was presented in the form of channel's helix frame possessing mobile dipole groups. The interaction of all mobile particles with the membrane channel's walls was taken into account. The calculation consisted of 50,0...

The DO1(18c6)fi (MwLi. Na. K and I 8c6=18-crown-6) complexes have been chosen as the model systems toinvestigate the nature of chemical bonds between alkali metal cations and large mffitidentaie orgmnic ligands.The B3LYP/6-3I+G(d,p) level of calculation has been used for obtaining equilibrium geernetnes and p(r)functions (electron density distributions). By the aid of fundamental physical theor...

It is shown that the "two-libron" lines in the Raman spectrum of solid hydrogen result from the large cubic anharmonicity of the quadrupole-quadrupole Hamiltonian. A localized picture is used to describe the interaction of two librational excitations on neighboring molecules, and dynamic interactions with other molecules are treated perturbatively. In this approximation the average single-libro...

An ab initio investigation of the optical constants of 9-Methyl-3-Thiophen-2-YI-Thieno [3,2e] [1,2,4] Thriazolo [4,3c] Pyrimidine-8-Carboxylic Acid Ethyl Ester crystal is performed within a framework of local density approximation (LDA), and the Engel-Vosko generalized gradient approximation (EV-GGA) exchange correlation potentials. It is established that there are two independent molecules (A ...

The thermodynamic functions such as enthalpy, H°, Gibbs free energy, G°, and entropy, S°, of Arginine and Lysine amino acids were theoretically studied at different polar solvents by using ²Gaussian o3², software. First, the structural optimization of isolated Arginine and Lysine were done in the gas phase by applying the Density Functional Theory (B3LYP) level ...

In thermodynamically characterizing a mixture comprising finite number of molecules, we consider two kinds protocol for producing from pure substance. The first is single alchemical operation, whereas the second series processes with feedback control in information thermodynamics and conventional mixing semipermeable membranes. A comparison numerically determined free-energy changes provides co...