Molecular Modeling Methods in the Development of Affine and Specific Protein-Binding Agents.

High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules.

Trapping and thermal migration of the first- and second-row atoms in Ar, Kr and Xe crystals.

Trapping and temperature-induced migration (TIM) of the first- and second-row atoms A from H to Ne in the face-centered cubic rare gas RG = Ar, Kr and Xe crystals are investigated within the classical crystal model parameterized by the empirically modified pairwise potentials. New coupled cluster A-RG potentials computed in a uniform way for all the atoms A are used to represent the atom-crystal interactions. Absolute and relative stabilities of the substitutional and interstitial trapping sites, their structures, interstitial migration pathways, related activation energies and rough estimates of the TIM rates are obtained.

Modeling of the thermal migration mechanisms of atomic oxygen in Ar, Kr, and Xe crystals.

Accommodation and migration of the ground-state (2s2pP) oxygen atom in the ideal Ar, Kr, and Xe rare gas crystals are investigated using the classical model. The model accounts for anisotropy of interaction between guest and host atoms, spin-orbit coupling, and lattice relaxation. Interstitial and substitutional accommodations are found to be the only thermodynamically stable sites for trapping atomic oxygen.

Stable axially symmetric atomic impurity in an fcc solid-Ba in rare gases.

Closed-shell metal atoms in rare gas solids tend to occupy highly symmetric polyhedral crystal sites, as follows from the generic triplet Jahn-Teller splitting of the S → P excitation bands and complies with the isotropic nature of the dispersion forces. Atypical 2 + 1 Jahn-Teller splitting inherent to axially symmetric sites observed recently for Ba atoms has been therefore interpreted as the defect accommodation. By modeling the structure, stability, and spectra of the Ba atom in the face-centered cubic rare gas crystals, we identify thermodynamically stable crystal site of axial C symmetry that explains experimental observations.