Simulation of Doxorubicin Delivery via Glucosamine(ethylene glycol) Carrier

This article focuses on the molecular modeling of the release of doxorubicin from capsules composed of glucosamine(ethylene glycol) oligomers. Doxorubicin forms micelle structures with glucosamine(ethylene glycol), and the drug release mechanism can be studied through the modeling of oligomeric bond breaking under acidic, neutral, or basic conditions. Under these conditions, the activation energies were calculated to be 145.51, 135.78, and 287.60 kcal/mol, respectively, at the B3LYP/6-31G//PM3 level. Based on these values, doxorubicin can be released into acidic and neutral solutions but not into basic solution. Ethylene glycol chain length in glucosamine(ethylene glycol) also effects drug release. As the length of ethylene glycol increases, the amount of drug released increases under acidic conditions, but decreases under neutral and basic conditions. When the drug is released from glucosamine(ethylene glycol) oligomers, the drug molecule and glucosamine(ethylene glycol) molecules form a micelle structure. Studies found that, as the length of the ethylene glycol chains increases, the micelle structure is more easily formed. The ethylene glycol group can deliver doxorubicin to cancer cells in micelle form

Binding and Docking Interactions of NO, CO and O2 in Heme Proteins as Probed by Density Functional Theory

Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O2 with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, whereas indirect interactions result by ligands in the same coordination sphere. Interactions play a crucial role in stabilizing transition states in catalysis or altering ligation chemistry. We have probed, by Density Functional Theory (DFT), the perturbation degree in the stretching vibrational frequencies of CO, NO and O2 molecules in the presence of electrostatic interactions or hydrogen bonds, under conditions simulating the inner cavities. Moreover, we have studied the vibrational characteristics of the heme bound form of the CO and NO ligands by altering the chemistry of the proximal to the heme ligand. CO, NO and O2 molecules are highly polarizable exerting vibrational shifts up to 80, 200 and 120 cm−1, respectively, compared to the non-interacting ligand. The importance of Density Functional Theory (DFT) methodology in the investigation of the heme-ligand-protein interactions is also addressed

Application of TD-DFT Theory to Studying Porphyrinoid-Based Photosensitizers for Photodynamic Therapy: A Review

An important focus for innovation in photodynamic therapy (PDT) is theoretical investigations. They employ mostly methods based on Time-Dependent Density Functional Theory (TD-DFT) to study the photochemical properties of photosensitizers. In the current article we review the existing state-of-the-art TD-DFT methods (and beyond) which are employed to study the properties of porphyrinoid-based systems. The review is organized in such a way that each paragraph is devoted to a separate aspect of the PDT mechanism, e.g., correct prediction of the absorption spectra, determination of the singlet–triplet intersystem crossing, and interaction with molecular oxygen. Aspects of the calculation schemes are discussed, such as the choice of the most suitable functional and inclusion of a solvent. Finally, quantitative structure–activity relationship (QSAR) methods used to explore the photochemistry of porphyrinoid-based systems are discussed

How Many Ligands Can Be Bound by Magnesium–Porphyrin? A Symmetry-Adapted Perturbation Theory Study

The stability of complexes of magnesium–porphyrin with one or two identical ligands from the set water, pyridine, imidazole, acetate, acetonitrile, dimethyl sulfoxide (DMSO), ethyl acetate, or acetylacetone was examined using symmetry-adapted perturbation theory (SAPT) for minimum geometries obtained by density-functional theory (DFT). The nonadditive contributions to the interaction energy of the porphyrin ring with two ligands were also included and found to be very small in almost all cases. The stability of the complexes under standard conditions is predicted on the basis of the free Gibbs energy. The analysis of individual components of the SAPT interaction energy allows us to explain why the complexation of the second ligand is not energetically preferred in some cases

Association Complexes of Calix[6]arenes with Amino Acids Explained by Energy-Partitioning Methods

Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes