Quantum and molecular mechanics calculations on modified silica nano ring

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

MODELING OF INTERFACIAL BEHAVIOR OF WATER AND ORGANICS

Modeling of water structure at a surface of different adsorbents, as well as an influence of dissolved compounds or co-adsorbates on bound water, is of importance to understand the temperature dependence of the characteristics of bound water, especially at T < 273 K, in comparison with bulk water. 1 H NMR spectra giving useful information on the water structure can be obtained using different ways such as experimental measurements, direct ab initio and density functional theory (DFT) calculations or estimation using semiempirical calculations and appropriate calibration functions. Here, application of the last approach is analyzed with respect to a variety of relatively large hydrated systems. Despite the simplicity of this approach, it gives quantitative characterization of structural features of interfacial water and effects of different co-adsorbates and adsorbent surfaces on bound water.

Intermolecular Interactions as Controlling Factor for Water Sorption into Polymer Membranes

A multidisciplinary approach was used for delineating the mechanisms controlling water sorption into modified block co-poly-(ether/amide) (PEBAX) membranes. In particular, incorporation of aromatic sulfonamide (KET) into the polymer matrix led to a nonlinear increase of water sorption in the membrane. The modification in sorption was accompanied by a nonlinear behavior in membrane surface energies. Infrared analysis revealed a different availability and accessibility of free polar groups supporting the formation of hydrogen bonding as a function of modifier concentration. A combination of both experimental and theoretical procedures was used to analyze the molecular processes of water sorption on PEBAX membranes. Molecular dynamics (MD) and quantum chemical (QC) calculations demonstrated that the formation of KET-KET dimers in the polymeric matrix led to a decrease in the interaction energy between water and modifiers. In addition, no variations in the dipole moments of water-dimer structures were found in comparison to a single KET and water-KET molecule. The formation of water-dimer complexes at higher concentration of modifier decreases the number of the dipole moment, thus preventing the polarization of polymer chains.