Molecularly imprinted polymers can be anticipated as synthetic imitation of natural antibodies, receptors and enzymes. In case of successful imprinting the selectivity and affinity of the imprint for substrate molecules are comparable with those of natural counterparts. The selection of the optimal functional monomer, monomer/template ratio as well as choosing of polymerization solvent is crucial determinants of the successful imprinting. In the present study the simulation approach to the development of molecular imprinting polymers for the extraction of new protein kinase ATP-competitive inhibitors is presented. By imprinting tri-O-acetyladenosine into polymer matrix the synthetic reproduction of adenosine triphosphate binding site to protein kinases can be fabricated and further used for adenosine triphosphate analogs screening in different sources. The optimized geometrical structure and energy of the pre-polymerization complexes of tri-O-acetyladenosine (template) with three different monomers-methacrylic acid, 3-vinyl benzoic acid and acrylamide in vacuum were calculated using hybrid quantum mechanical/molecular mechanical (QM/MM) approach. These calculations demonstrate that methacrylic acid forms the most stable complex with template, the next is 3-vinyl benzoic acid complex and the third-acrylamide one. The bond energies of the complexes are shown to increase monotonically as more monomers are linked to the template. The same conclusions are made from purely quantum self-consistent field calculations of pre-polymerization complex energy and structure. Hybrid calculation is shown to be effective and can substantially accelerate the development of the imprinting technology.

Molecular imprinting is a promising way to create polymer materials that can be used as artificial receptors, and have anticipated use in synthetic imitation of natural antibodies. In case of successful imprinting, the selectivity and affinity of the imprint for the substrate molecules are comparable with those of natural counterparts. Various calculation methods can be used to estimate the effects of a large range of imprinting parameters under different conditions, and to find better ways to improve polymer characteristics. However, one difficulty is that properties such as hydrogen bonding can be modeled only by quantum methods that demand a lot of computational resources. Combined quantum mechanics/molecular mechanics (QM/MM) methods allow the use of MM and QM for different parts of the modeled system. In present study this method was realized in the NWChem package to compare estimations of the stability of tri-O-acetyl adenosine-monomer pre-polymerization complexes in benzene solution with previous results under vacuum.

Carbon nanotubes are the basic element of modern nanoelectronic devices. One of the most promising their applications is a carbon nanotube based conducting channel in field-effect transistor with Si02 dielectric deposited on the nanotube. Simulation of SiO, on CNT technology and some properties of that system were studied by means of molecular dynamics method. MM+ interatomic potential was used for calculations.

The results of the computer simulations of certain electronic properties of the austenite phase of Ni-Mn-Ga alloy are presents. Cluster approach was used and both self-consistent and density functional methods were exploited.

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