BIOVIA MATERIALS STUDIO QMERADATASHEETBIOVIA Materials Studio QMERA offers modelers acomputationally effective approach for combining the accuracyof density functional theory (DFT) quantum mechanics withthe speed of a force field calculation. This hybrid approachmakes it possible to perform accurate calculations on verylarge systems using little computer time. It is particularly
well-suited for modeling problems in chemical reactivity,
where an active site is chemically localized. Researchers canuse the method to study problems in nanotubes, nanoclusters,
and amorphous material. BIOVIA Materials Studio QMERA
can be used to perform virtual experiments, leading totremendous reduction in costly lab-based experiments as well
as shorter developmental cycles. As part of the comprehensive
BIOVIA Materials Studio® (MS) software environment,
BIOVIA Materials Studio QMERA can be supplemented withsophisticated modeling and analysis tools that help users
attain even further insight into their systems of interest.

OVERVIEW
Understanding the chemistry of systems with a large number ofatoms is essential to improving products and processes in areas
such as nanotechnology, pharmaceuticals, petrochemistry,catalysis, and fine and specialty chemicals. In the field ofcatalysis, for example, it is important to understand how areaction proceeds at a particular site on a metal surface or in
the pore of a zeolite. Similarly, in drug discovery, one would
like to understand the reaction paths that lead to a drug being
metabolized. These types of systems–with a localized active
site surrounded by a large number of atoms that can influence
the reactivity–are ideal applications for hybrid quantum
mechanical (QM)/ molecular mechanical (MM) approaches,
which combine the accuracy of quantum mechanics with thespeed of a force field calculation

THE BIOVIA MATERIALS STUDIO QMERAADVANTAGE—HYBRID QM/MMThe BIOVIA Materials Studio QMERA module in BIOVIA Materials
Studio performs simulations by combining DFT methods fromMS DMol31 and force field methods from MS GULP2.
BIOVIA Materials Studio QMERA can be used to model either
molecular or periodic systems and can handle hundreds or eventhousands of atoms. Use BIOVIA Materials Studio QMERA tostudy :• Organic molecules• Molecular crystals• Polymers• Organometallics• Nanotubes• Nanoclusters• Zeolites• Organic/inorganic interfaces• and more
It can be used to predict a variety of properties for these diversesystems; such as:• Structures• Reaction thermodynamics• Reaction kinetics• Electronic properties• Vibrational spectra

ABOUT THE BIOVIA MATERIALS STUDIODMOL3 DFT PROGRAMBIOVIA Materials Studio DMol3 is a DFT program with a longtrack record of successful commercial applications. With its
unique approach to solving quantum mechanical equations,
BIOVIA Materials Studio DMol3 has long been one of the fastest
methods available for performing calculations, an advantagethat becomes apparent especially for larger systems.

ABOUT THE BIOVIA MATERIALS STUDIO GULPFORCE FIELDSBIOVIA Materials Studio GULP implements a wide range ofpotential models, which spans both inorganic and organic
materials. The potentials include the shell model, the Universal
Force Field, the embedded atom method (EAM), and bondorder and reactive force fields. The Universal Force Field
makes it possible to perform BIOVIA Materials Studio QMERA
calculations using any element, including metals. The Sauer
Force Field provides particularly reliable results for zeolites, acommon application of QM/MM.

KEY USES OF BIOVIA MATERIALS STUDIO QMERAHeterogeneous and Homogenous Catalysts
BIOVIA Materials Studio QMERA allows the reactivity ofheterogeneous and homogeneous catalysts to be screened in
extremely fast, but reliable, calculations because it treats onlya small portion of the system using DFT. The time needed
to complete a geometry optimization with BIOVIA Materials
Studio QMERA could be roughly 1/8 of the time needed
to do the same calculation with pure DFT, yet the BIOVIA
Materials Studio QMERA calculation yields comparable reactionenergetics.

Treating the “chemically active” part of the system withquantum mechanics allows the electronic structure and itschanges (e.g. bond breaking and formation in a chemicalreaction) to be modeled using a minimum of computationalresources. The remaining portion of the system is describedusing molecular mechanics, with the two regions being allowed
to interact. The combination of the speed and efficiency of theMM force field calculations (for the bulk of the system) with theversatility and precision of the QM method (for the importantreactive zone) allows reactions in large systems to be studied
in a more realistic manner than would be possible using either
QM or MM alone.

Figure 1: A Ru(H)2(diphosphine)(diamine) complex
modeled by BIOVIA Materials Studio QMERA. BIOVIA
Materials Studio QMERA can model this systemefficiently, with only a fraction of the atoms treatedwith quantum mechanics, hence allowing fast, yetaccurate, calculations.

Virtual Screening of Candidate Materials
BIOVIA Materials Studio QMERA can be used to perform
virtual screening experiments of candidate materials. With thisfast hybrid technique, users can quickly screen candidates
and subject only the leading candidates to experimental
testing, thereby offering a lower cost alternative to performing
experimental testing of all possible candidates.
BIOVIA Materials Studio QMERA can be used to:• Screen multiple reagents• Propose modifications of a synthetic route• Test nanoclusters of different compositions for catalytic
activity• Probe multiple defect sites on a carbon nanotube (see Figure 2)

HOW DOES BIOVIA MATERIALSSTUDIO QMERA WORK?
BIOVIA Materials Studio QMERA is a program that allows
combined QM/MM force field calculations to be performed on
both periodic and non-periodic systems by using the ChemShell
environment.3 ChemShell is a computational chemistry
environment that employs a Tcl interpreter for communicationand data handling in hybrid QM/ MM calculations, leaving thetime-consuming energy evaluations to specialized external
codes like BIOVIA Materials Studio DMol3 and BIOVIA Materials
Studio GULP.

Figure 2: A study of the formation energy of aStone-Wales defect on a carbon nanotube
using BIOVIA Materials Studio QMERA .

BIOVIA Materials Studio QMERA provides both mechanical andelectronic embedding schemes for treatment of the QM/MMinteractions. Dangling covalent bonds between the QM andMM regions are capped with hydrogen “link” atoms, making
it possible to treat any type of chemical bond whatsoever.
Geometry and transition state optimizations in BIOVIA Materials
Studio QMERA can be carried out using a range of minimizers.

WHAT CALCULATIONS CAN BIOVIA MATERIALSSTUDIO QMERA PERFORM?
The BIOVIA Materials Studio QMERA module in BIOVIAMaterials Studio allows the user to perform hybrid calculations
using DFT and force fields. BIOVIA Materials Studio QMERA
can currently perform four different tasks:

The key to success of a mixed QM/MM calculation
involves the division of a system into two parts:• Single-point energy calculation• Geometry optimization• Transition-state optimization• Transition-state search• The central “chemically active” QM region• The surrounding “outer” MM region

Each of these calculations can be set up so that it generates
specified chemical and physical properties:• Atomic population analysis (Hirshfeld, Mulliken or electrostatically fitted charges)• Harmonic vibrational frequencies• Molecular orbitals (MOs)• Charge density• Electrostatic potential
A full list of the force fields and potentials available in BIOVIA
Materials Studio GULP is available on the BIOVIA Materials
Studio GULP webpage.

BIOVIA Materials Studio QMERA is part of the comprehensive
BIOVIA Materials Studio software environment. BIOVIA Materials
Studio provides a user-friendly interface that complies with
Windows standards, which together with a variety of trainingoptions, makes it easy for any user to learn the software withconfidence. On top of this, BIOVIA Materials Studio offers awealth of modeling and simulation tools that can be used tosupplement BIOVIA Materials Studio QMERA.
For example, BIOVIA Materials Visualizer—the core of BIOVIA
Materials Studio— offers a wide range of model building andvisualization tools that allow users to construct models of thesystems of interest, easily select the QM region, and run a QM/MM calculation. In particular, researchers in nanotechnology
will benefit from the nanotube builder, which can create single
walled, multi-walled and bundles of nanotubes, as well as thenanocluster builder, which can create spheres, tetrahedra, andother shapes.

On top of this, a flexible client-server architecture means that
calculations can be run on servers located anywhere on acompany’s network. Results are returned to a user’s PC, where
they may be displayed and analyzed. It is easy to produce
high quality graphics of molecular and materials structures, aswell as molecular orbitals. Structures, graphs and other data,such as video clips, can be instantly exchanged with other PC
applications, facilitating sharing among colleagues and analysis
in spreadsheets and other packages.
To learn more about BIOVIA Materials Studio, go toaccelrys.com/materials-studio

REFERENCES:
1. BIOVIA Materials Studio DMol3 module. Find details at:
http://www.accelrys.com/products/materials-studio/modules/dmol3.html
2. BIOVIA Materials Studio GULP module. Find details at:
http://www.accelrys.com/products/materials-studio/modules/GULP.html
3. P. Sherwood, A. H. de Vries, M. F. Guest, G. Schreckenbach, C. R. A. Catlow, S. A. French, A. A. Sokol, S. T.
Bromley, W. Thiel, A. J. Turner, S. Billeter, F. Terstegen, S. Thiel, J. Kendrick, S. C. Rogers, J. Casci, M. Watson,F. King, E. Karlsen, M. Sjøvoll, A. Fahmi, A. Schäfer and Ch. Lennartz. J. Mol. Struct.
(THEOCHEM), 2003, 632, 1.

BIOVIA Materials Studio also offers analysis tools thatcomplement BIOVIA Materials Studio QMERA. For example,
population analysis controls allow users to assign charges andspins and bond orders, while other tools allow users to display
3D renderings of molecular orbitals, charge densities, andelectrostatic potentials.

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THE BIOVIA MATERIALS STUDIO ADVANTAGE—TOOLS TO COMPLEMENT BIOVIA MATERIALSSTUDIO QMERA