Investigation of interactions of doxorubicin with purine nucleobases by molecular modeling.

Doxorubicin, an anthracycline antibiotic with anti-tumor activity, is produced by the bacterium Streptomyces peucetius. The interactions between doxorubicin and genetic material and the details of the intercalation with DNA have been controversial issues. Thus, the interactions of doxorubicin with purine nucleobases were studied by quantum mechanical methods.

DFT and TDDFT investigation of the Schiff base formed by tacrine and saccharin.

Schiff bases have many chemical and biological applications in medicine and pharmaceuticals due to the presence of an imine group (-C=N-). These bases are used in many different fields of technology, and in photochemistry because of their photochromic properties. Here, the structural and electronic properties of the Schiff base formed by tacrine and saccharin (TacSac) were explored using density functional theory with the B3LYP, M06-2X, M06L, and ωB97XD functionals in combination with the 6-311++G(d,p) basis set.

Modeling prepolymerization step of a serotonin imprinted polymer.

Studies on generating artificial macromolecular receptors by molecular imprinting of synthetic polymers significantly emerged in the literature during last decades. The non-covalent approach, one of the three methods used in MIP synthesis, is more flexible for the choice of functional monomers, possible target molecules, and use of the imprinted materials. This study aims to investigate a serotonin imprinted polymer prepared by non-covalent approach using molecular modeling.

Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level.

NO binding to cobalamin: influence of the metal oxidation state.

Density functional and molecular orbital theory calculations on models for cobalamin suggest that NO binds similarly to the Co(II) and Co(III) oxidation states. However, Co(III) can bind water far more strongly than Co(II) as a sixth ligand, so that the competition between water and NO complexation strongly favors water for Co(III) in the gas phase. Although the Co(II) oxidation state is found to bind water slightly more strongly than NO in the gas phase, the inclusion of solvation effects via the polarizeable continuum model makes NO binding more favorable.

AM1* parameters for phosphorus, sulfur and chlorine.

An extension of the AM1 semiempirical molecular orbital technique, AM1*, is introduced. AM1* uses AM1 parameters and theory unchanged for the elements H, C, N, O and F. The elements P, S and Cl have been reparameterized using an additional set of d orbitals in the basis set and with two-center core-core parameters, rather than the Gaussian functions used to modify the core-core potential in AM1.

A study on the structures of the substituted (aminomethyl)lithium and (thiomethyl)lithium compounds.

The structures of substituted (aminomethyl)lithium and (thiomethyl)lithium compounds have been examined. Geometric parameters, charge densities, bond orders, dipole moments and heats of formation for all the members of the two series of monomers and dimers of the units LiCN(R)2 and LiCSR where R=H, CH3(Me), C6H5(Ph) have been calculated. The structures of the three complex compounds containing the same units; [[Li(CH2SMe)(THF)]X], [Li2(CH2SPh)2(THF)4] and [Li2(CH2NPh2)2(THF)3] have also been modeled.