Software Material Studio

Membrane-Interaction (MI)-QSAR approach developed by Iyer et al. was used to develop predictive models of some organic compounds through BBB, and to simulate the interaction of a solute with the phospholipide-rich regions of cellular membranes surrounded by a layer of water. Molecular dynamics simulations were used to determine the explicit interaction of each test compound with the DMPC-water model (a model of dimyristoylphosphatidylcholine membrane monolayer, constructed using the software Material Studio according to the work done by van der Ploeg and Berendsen). Six MI-QSAR equations were constructed (Eqs. 74-79) ... 

Materials Studio is a software environment that brings together the world s most advanced materials simulation and informatics technology. It is a product of Accelrys Inc. 

Materials Studio 4.0., Accelrys Software, Inc., San Diego (licensed to Nicolae Hurduc)... 

Rietveld refinement programs are included in software products sold by Broker (http //vmw.bruker-axs.com/production/indexnn.htm), Philips (http //wvm-us.analytical. philips.com/products/xrd/), Rigaku/USA (http //vmw.RigakuMSC.com/xrd/index.shtinl), STOE Cie, Gmbh (http //vmw.stoe.com/products/index.htm). Reflex or Reflex+ modules in Materials Studio or Cerius2 suites from Accelrys Inc. (vmw.accelrys.com). Jade and jPOWD from MDI, Materials Data Inc. (vmw.materialsdata.com) and others. 

Materials Studio A software for modeling and simulation of crystal structure, polymer properties, and structure-activity relationships (http //www.accelrys.com/products/mstudio)... 

With the increased availability of software (e.g., DISCOVER in CERIUS by Materials Studio, ETOMICA Kofke and Mihalick, 2002) and faster computers, these simulations are being carried out more routinely for the estimation of thermophysical and transport properties, as well as for the calculation of phase equilibria. The estimates are tuned to match experimental data by adjusting the energy and size parameters. 

The 12 molecular models taken from the conformational search in the earlier section were partially geometry optimized using the code DMoP [32] (VWM-BP/DNP level of theory) implemented in the Material Studio software package [33]. For this, torsion angles were fixed and atomic point charges were derived to fit the molecular surface electrostatic potential (ESP) for these initial conformations. 

FIGURE 6.12 Crystal morphology of ibuprofen in isolation of solvent environment predicted using Materials Studio software. 

A crystal morphology simulation for ibuprofen was performed with Accelrys s Materials Studio software suite, utilizing the morphology module. The crystal structure was originally obtained from the CSD and then fully optimized using the COMPASS force field—a priori to morphological calculations. As shown in Figure 6.12, the unrelaxed vacuum slabs of crystal faces with thickness of 25 A were constructed from the optimized crystal stracture. 

Accehys. Materials Studio, 6.0. Accelrys Software Inc. San Diego, 2015. 

In Fig. 9.6 the execution of algorithm MSG in software PNS Studio excludes operation unit D8 from consideration. The modeling mistake identified is that only the major product of the process material S19 is labeled as product, while the other two, S09 and S20, are not. As a consequence, operating unit D8 is eliminated in the light of axiom (S4). 

The second modeling mistake illustrated is the definition of the starting raw material as intermediate material, thus eliminated according to axiom (S2) because of the absence of any operating unit producing it. Subsequently, all the initial structure is excluded from the consideration indicated as ERROR There is no maximal structure. by algorithm MSG in software PNS Studio in Fig. 9.7. 

Fig. 1. A molecular model of a condensed phase polymer blend. The example shown is used to study a mixture containing atactic polystyrene 40-mer (2 chains) and atactic poly(methyl methacrylate) 40-mer (2 chains). Figure la shows the cell with the molecules configured as they are in space the parts of the molecules lying outside the cell occupy adjacent cells in the periodic structure. To convey the space filling nature of the construction, Figure lb shows the same molecules packed in the cell. The model system was constructed using the Amorphous Cell module in the Materials Studio software package distributed by Accelrys (103). The amorphous cell system was constructed at a density of 1.12 g/cm at 300 K and the subsequent 80 ps of NPT dynamics at the same temperature and zero pressure equilibrated the system to a density of 1.057 g/cm .

During the last 40 years, computer-based computational methods, such as molecular dynamics and Monte Carlo simulations, have evolved from advanced techniques accessible only to a few speciahsts, to standard calculation approaches available to both scientists and engineers. Similarly, numerical methods of solving the Schrodinger equation, implemented in computational softwares such as Gaussian or Materials studio, are now commonly used to study complex systems. Proper modehng of those systems plays more and more important role in modem scientific research. 

Accelrys Software hic. (2013) Material studio, release 6.1. Accehys Software Inc., San Diego... 

Polymer models were created using the Amorphous Cell module of the Materials Studio suite of software based on the self-avoiding random walk method of Theodorou and Suter and on the Meirovitch scanning method. Amorphous cis-PBD three-dimensional (3D) models consisted of 10 chains of 30-monomer oligomers and were equilibrated using a temperature cycle protocol under periodic boundary conditions (Figure 9.1). For a full description of the methodology used to build the equilibrated polymer models at various temperatures, please see Ref. [7]. 

Solvation behavior can be effectively predicted using electronic structure methods coupled with solvation methods, for example, the combination of continuum solvation methods such as COSMO with DFT as implemented in DMoF of Accelrys Materials Studio. An attractive alternative is statistical-mechanical 3D-RISM-KH molecular theory of solvation that predicts, from the first principles, the solvation structure and thermodynamics of solvated macromolecules with full molecular detail at the level of molecular simulation. In particular, this is illustrated here on the adsorption of bitumen fragments on zeolite nanoparticles. Furthermore, we have shown that the self-consistent field combinations of the KS-DFT and the OFE method with 3D-RISM-KH can predict electronic and solvation structure, and properties of various macromolecules in solution in a wide range of solvent composition and thermodynamic conditions. This includes the electronic structure, geometry optimization, reaction modeling with transition states, spectroscopic properties, adsorption strength and arrangement, supramolecular self-assembly,"and other effects for macromolecular systems in pure solvents, solvent mixtures, electrolyte solutions, " ionic liquids, and simple and complex solvents confined in nanoporous materials. Currently, the self-consistent field KS-DFT/3D-RISM-KH multiscale method is available only in the ADF software. 

Accelrys. Materials Studio Release Notes, Release 4.1. Accehys Software, San Diego, CA, 2006. 

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