Materials Studio Application Example Webinars

Webinar Abstracts

Mesoscale modelling of precipitation membranes and carbon nanotubes (was Polymers and Simulation)

This webinar will be based on recently published work by Accelrys Scientists focusing on mesoscale modeling. Applications will include an extension to our current DPD code for simulation of rigid bodies and a study of polymer precipitation membranes using MesoDyn.

Predicition of crystal structures & properties: combining density functional theory, experiment, and empirical methods

Predicting the structure of crystals remains an significant challenge. This is especially true in pharaceutical chemistry where different crystal polymorphs may exhibit significantly different activity. Crystal structures are often derived from x-ray data. Force field methods can be used to refine the predicted structure and to predict crystal morphology. However, the energy differences between possible structures are very small, and these methods may not be able to discriminate among low-lying structures, nor do they take into account temperature effects.

Quantum mechanical based methods such as density functional theory (DFT) are much better at predicting structures from first principles and at discriminating among energetically low-lying structures; but they are computationally intensive, and so cannot sample as many potential crystal structures as a force field method.

An effective approach results from combining the methods. Low lying polymorphs may be determined by force field methods and refined by DFT to provide a more reliable predictions. DFT can, in addtion, predict analytical results such as IR and NMR spectra. Comparing these results to experiment provides additional means of discriminating among possible crystal structures. The IR may, in addition, be used to predict phase stability as a function of temperature. The webinar will present an examples in which polymorph stability is predicted to change as temperature increases.

Nanobio-technology: materials impact on bio, and bio impact on materials

Join Accelrys scientists from life and materials science for this exciting interdisciplinary webinar demonstrating how modeling and simulation at the quantum, atomistic and mesoscale level contributes to our understanding of important issues in nanobio-technology, with applications from health care to electronics. Case studies discussed include:

• molecular design of biosensors,
• temperature dependent mesophase changes in amphiphilic dendron molecules with applications from electronics to drug delivery, and
• detailed analysis of buckyball/antibody binding via molecular dynamics simulation.

Solving Inorganic Crystal Structures with Reflex Plus

The procedure comprises several steps which are accounted for by different tools in Reflex Plus, namely, Powder Indexing, Powder Refinement and Powder Solve. The indexing of the powder pattern is followed by the determination of the space group and the refinement of the cell parameters, peak shape and background parameters by a modified Pawley method. Then a global optimisation algorithm - either Monte Carlo Simulating Annealing or parallel tempering - is used to generate trial structures in direct space finding the solution that maximizes the agreement between the simulated and experimental powder diffraction pattern. Such agreement is measured by a full-profile comparison using the R wp factor.

One of the recent improvements of Reflex Plus is the ability to deal with atoms occupying special positions, which is common in inorganic crystals. Application examples of systems with different complexity, including framework structures like zeolites and layered aluminophosphates, will be discussed.

Advanced Simulations using Discover

Here we take a look at advances in atomistic simulations for molecular systems and materials, exploring the relationship between structure and molecular behaviour, molecular interactions and the prediction of key properties in solids, liquids and gases.

Optimal use of Materials Visualizer and the Study Table

In the last few releases of Materials Studio (MS) Modeling, there have been several new tools added to Materials Visualizer, the core component that provides modeling, analysis, and visualization tools used to support the full range of MS Modeling products. Recent additions to Materials Visualizer have included a new document type, the Study Table, atom volumes and surfaces, and a new atom positioning tool. This webinar will show you how to get the most out of these new tools.

MesoProp: Get More from your Mesoscale Simulations!

MesoProp is a brand new tool available from Accelrys. Developed by MatSim GmbH, MesoProp uses morphologies calculated from Accelrys' mesoscale tools, DPD and MesoDyn, to predict engineering properties of multiphase systems. This webinar will examine how MesoProp can be used to calculate properties based on mesoscale input and give examples of a worked application of MesoProp. Customers who currently have mesoscale tools should attend this webinar to find out how they can get more from their mesoscale simulations. Nanotechnology and the Nanotechnology Consortium: new tools and ongoing developments

The webinar will provide an update on the status of the Consortium and a presentation of new software tools recently developed by the Consortium. These include new Nanostructure Builders, GULP interface, and ONETEP, the novel linear-scaling DFT method. An outline of current development projects will also be given.

New Tools for Quantum Mechanics: Doing DFT the Easy Way

Materials Studio 3.2 provides new tools that help integrate quantum mechanical calculations into your workflow. A Study Table can now be used to launch multiple DMol 3 jobs, correlate the results, and provide DFT-based descriptors for QSAR analysis. This greatly simplifies the task of setting up calculations, as well as streamlining the process of analysis. In addition, simulation of IR spectra is available, providing a facile means of comparing computed and experimental results.

QSAR is a technique that has been widely used in pharmaceutical research and is recently being applied in the materials science industries. Using DFT, one can obtain descriptors for a wide range of materials including molecules, as well as periodic solids like molecular crystals, zeolites, and metals. Several examples of using the study table to manage jobs will be demonstrated, and the results will be analyzed with QSAR methods.

Crystal Structure Determination using Reflex Plus OR Close contact penalty functions in direct space methods and energetic considerations in structure refinement

When solving crystal structures from powder diffraction data using direct space methods, all available information (i.e., molecular structure and space group symmetry) is used to limit the number of degrees of freedom. When the quantity of information available from a powder diffraction diagram is limited (due to, e.g., broad peaks, preferred orientation, positions of weak scatters like H atoms…) and/or the number of degrees of freedom is large, it may be necessary to add extra chemical information to the process in order to obtain a solution. This extra chemical information can be introduced by requiring the generated structures to be energetically stable. In this scenario, the potential energy contributes to a combined figure of merit alongside the powder pattern similarity, R wp . Higher energy structures then have a higher value for the combined figure of merit and are therefore penalized during the optimization process.

One of the most basic pieces of chemical information that can be incorporated into a structure determination is to utilize the fact that viable solutions should not contain overlapping atoms. Adding a simple close contact penalty that prevents solutions with non-viable intermolecular interactions from being generated is adequate for the global optimization process, which aims at locating a rough, refinenable solution. The close contact penalty model implemented in Reflex Plus will be discussed, including a number of case studies where the use of this feature has made the derivation of crystal structure solution possible.

During refinement an accurate description of the potential energy (e.g. a good force field) should be used in combination with the R wp in a weighted optimization process. The a priori determination of the weighting factor might not be intuitive; in such cases a Pareto optimization ( a posteriori preference articulation) can be used to obtain an appropriate value. It will be demonstrated, how the use of the R wp factor in conjunction with energies derived from a force field expression can be used in an all-atom Rietveld refinement process to determine structures that are both chemically viable and in close agreement with the experimental powder pattern.

Using materials QSAR to get the most from your experiments

QSAR is a technique that has been widely used in the discovery process in pharmaceutical research. However, there are also many applications in the chemical and materials science industries. This webinar will talk about applications of QSAR in the Materials Science area and look in detail at the additives industry. It will cover the QSAR process, discuss new features available in MS Modeling 3.2, and answer the question of why we should all be using QSAR.

Development and application of BTcl simulation protocols for study of alcohol and alkane nanofilms confined between metal oxide surfaces

Two areas of molecular modeling in which there has been significant progress over the past several years include direct simulation of the shearing of liquids confined in narrow channels, and development of force fields capable of making thermophysical property predictions over wide ranges of temperature and pressure with an accuracy comparable with experiment.

In view of mounting interest in manipulating and understanding nano-devices in which characteristic dimensions lie on the range of tens to hundreds of Angstroms, a natural development of the earlier shear simulation work is the direct simulation of increasingly complex systems using chemically realistic and accurate intra and intermolecular potentials. Consequently in our ongoing research, we have developed and applied Discover BTcl simulation procedures and have used these in conjunction with the state-of-the art COMPASS force field to examine the behavior of liquids confined between the types of surfaces found in actual systems. These procedures can be conveniently accessed through the Amorphous Cell module of MS Modeling.

This webinar will focus on molecular simulation studies of liquids confined at either iron oxide or iron surfaces. Specifically, we will discuss the key features of the simulation protocol and will compare the behavior of confined linear C13 alkane molecules with that of chains of the same length terminated by either one or two hydroxy groups, in which there exists the possibility of specific interactions with the surface in addition to intermolecular and, in the case of the diol, intramolecular hydrogen bond formation.

The interplay of these various types of interaction will be discussed both for static confined films at equilibrium, and for systems in which shear is applied. Results will be presented for the effects of specific interactions on the rheological, thermodynamic and structural properties of these thin films of alkanes and alcohols.

The research was performed in collaboration with Dr. R.S. Khare, University of Wisconsin.

Molecular modeling for generic drug development

Accelrys' technology can give you the advantage in the race of Abbreviated New Drug Applications (ANDAs) through:

• Determining physiochemical property prediction and polymorphism
• Enhancing your batch-to-batch quality control through material characterization
• Improving your product performance through excipient selection and screening of chemical incompatibility
• Ensuring your processability and manufacturability through material morphology prediction and analysis of the effects of processing parameters.

By viewing our presentation you'll see the workings of these tools, including their application to real-life scientific examples.

Applying QSAR techniques to problems with chemical and materials R&D

A free web-based seminar on the use of quantitative structure activity relationship (QSAR) methods to study practical problems in materials and chemicals research.

QSARs methods allow you to establish mathematical relationships between key physicochemical properties of materials and features of the system, such as chemical or geometrical structure. You can then apply these relationships to predict and understand properties. QSAR provides a fast and efficient means to identify, screen, and optimize candidate compounds and materials.

The seminar explains how QSAR techniques contribute to solving key R&D issues with real-life case studies demonstrating the scope of the tools.

Applying classical simulation tools to study interactions at surfaces

Classical simulation methods employ parameterized forcefields which avoid the size restrictions of quantum mechanics methods. They approximate molecules as structures consisting of balls (atoms) connected by springs (bonds). This approximation allows simulations of thousands of atoms over nanoseconds of time giving the ability to predict many bulk physical properties.

This seminar explains how classical simulation methods can be used to study physical interactions at surfaces with attention to the paints, coatings, and adhesives industries. Background, the different types of applications, and a worked example are illustrated.

Understanding the electronic and magnetic properties of Materials: what's new with MS Modeling 3.1

Materials Studio's MS Modeling 3.1, released October 2004, contains a number of exciting tools for studying the electronic structure of molecules, periodic solids, and interfaces. Leading the list of developments is the release of NMR CASTEP, a method for the first-principles prediction of NMR chemical shifts and electric field gradient tensors. The method can be applied to compute the NMR shifts of molecules, solids, interfaces, and surfaces for a wide range of materials classes including organic molecules, ceramics, and semiconductors. As an example, the Webinar will focus on the assignment of 17O chemical shifts in silicates.

Other new developments include the ability to simulate Scanning Tunneling Microscopy (STM) in CASTEP, and the ability to compute charge density differences. Both advances allow researchers to understand, in a simple, visual manner, how the electron density affects the structure of complex systems. The STM images allow direct comparison with experiment. Charge density differences allow users to see how the density relaxes between two complex systems, for example between a molecule and a surface. The webinar will cover several examples of atoms & molecules absorbed on metal and metal oxides surfaces.

Computer-aided nanotechnology (CAN): recent applications and overview of the first Nanotechnology Consortium Meeting

Computer-aided Nanotechnology describes the concept of utilising computational tools to support a design approach to the development of nanomaterials and devices.

'Nanomaterials by Design' is one of the 'Grand Challenges' by the US National Nanotechnology Initiative. A recent roadmap published by the US Chemical Industry Vision2020 Technology Partnership, identifies Modeling and Simulation, and its integration with areas such as synthesis, characterization, and manufacturing as key to taking nanotechnology from its current scientific discovery stage to an engineering discipline.

Today, Accelrys' MS Modeling software already offers a range of tools, which support many aspects of nanotechnology research, including for example the new NMR and STM (Scanning Tunneling Microscopy) capabilities in the MS Modeling 3.1 release.

Further increasing accuracy and building bridges between Accelrys' current chemistry software tools and complementary engineering design tools are the focus of the new Accelrys Nanotechnology Consortium. In particular, the Consortium develops software tools to improve the specification of nanoscale systems (builders, protocols), to address larger size and time scales in systems involving quantum phenomena, to link to metrology and characterisation via instrument simulation, and to improve integration with engineering applications.

The webinar provides an example of a recent nanotech application using MS Modeling, and an overview of the current developments and plans of the Nanotechnology Consortium presented at the first annual meeting in New York.

Materials Engineering: Connecting the lengths scale from atomistic to finite element

Atomistic simulation methods have advanced over many years, and allow one to predict the properties of a range of materials. High quality atomistic force fields, developed from quantum mechanics simulations, make possible the prediction of bulk properties such as density and solubility parameters, as well as other properties such as surface binding energies. One can perform more coarse grain mesoscale simulations with MS Modeling software in order to predict the morphologies of complex composite materials. In a mesoscale model, atoms are no longer present, and a single particle is used to represent a collection of atoms, or a segment of a polymer chain. Such models allow one to study the structure of mixtures of soft materials such as polymers and surfactants up to the micron size scale, and to predict properties such as the surface tension between liquids. The parameters describing the interaction between the various particle types which represent the mixture components can be derived from atomistic simulation. Thus, the length scales of electronic structure described by quantum mechanics simulations, to atomistic force fields, and ultimately mesoscale simulations, are connected.

It is now possible to connect mesoscale simulations with engineering property prediction methods, in order to predict engineering properties of complex mixtures. This is done by using morphology models derived in a mesoscale simulation, as input to a finite element analysis method. This webinar will describe a new simulation tool, MesoProp, which takes as input the morphology models generated by Accelrys' mesoscale simulation methods, MS MesoDyn, and Dissipative Particle Dynamics, and predicts mechanical, thermal, and gas diffusivity properties of complex mixtures. Through the MesoProp software, one can select the properties of the pure component phases, load in the mesoscale simulation model, and then calculate engineering properties for the composite. Examples of the use of the use of these mesoscale and finite element analysis methods together will be described.